Implement core clustering logic and scoring features

This update introduces the core clustering algorithm, including parallel execution, dynamic block sizing, and SIMD-accelerated scoring methods. It also adds robust sequence preparation, k-mer analysis, and comprehensive test data fixtures for validation.

cmd/obitools/obiclust/main.go

@@ -0,0 +1,28 @@
+package main
+
+import (
+	"os"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiclust"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
+)
+
+func main() {
+	optionParser := obioptions.GenerateOptionParser(
+		"obiclust",
+		"star clustering of sequences (the algorithm of sumaclust, UCLUST and CD-HIT)",
+		obiclust.OptionSet)
+
+	_, args := optionParser(os.Args)
+
+	fs, err := obiconvert.CLIReadBioSequences(args...)
+	obiconvert.OpenSequenceDataErrorMessage(args, err)
+
+	clustered := obiclust.CLIOBIClust(fs)
+
+	obiconvert.CLIWriteBioSequences(clustered, true)
+
+	obiutils.WaitForLastPipe()
+}

obitests/obitools/obiclust/test.sh

@@ -0,0 +1,188 @@
+#!/bin/bash
+
+#
+# Here give the name of the test serie
+#
+
+TEST_NAME=obiclust
+CMD=obiclust
+
+######
+#
+# Some variable and function definitions: please don't change them
+#
+######
+TEST_DIR="$(dirname "$(readlink -f "${BASH_SOURCE[0]}")")"
+OBITOOLS_DIR="${TEST_DIR/obitest*/}build"
+export PATH="${OBITOOLS_DIR}:${PATH}"
+
+MCMD="$(echo "${CMD:0:4}" | tr '[:lower:]' '[:upper:]')$(echo "${CMD:4}" | tr '[:upper:]' '[:lower:]')"
+
+TMPDIR="$(mktemp -d)"
+ntest=0
+success=0
+failed=0
+
+cleanup() {
+    echo "========================================" 1>&2
+    echo "## Results of the $TEST_NAME tests:" 1>&2
+
+    echo 1>&2
+    echo "- $ntest tests run" 1>&2
+    echo "- $success successfully completed" 1>&2
+    echo "- $failed failed tests" 1>&2
+    echo 1>&2
+    echo "Cleaning up the temporary directory..." 1>&2
+    echo 1>&2
+    echo "========================================" 1>&2
+
+    rm -rf "$TMPDIR"  # Suppress the temporary directory
+
+    if [ $failed -gt 0 ]; then
+       log "$TEST_NAME tests failed" 
+        log
+        log
+       exit 1
+    fi
+
+    log
+    log
+
+    exit 0
+}
+
+log() {
+    echo -e "[$TEST_NAME @ $(date)] $*" 1>&2
+}
+
+log "Testing $TEST_NAME..." 
+log "Test directory is $TEST_DIR" 
+log "obitools directory is $OBITOOLS_DIR" 
+log "Temporary directory is $TMPDIR" 
+log "files: $(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2)"
+
+######################################################################
+####
+#### Below are the tests
+####
+#### Before each test :
+####  - increment the variable ntest
+####
+#### Run the command as the condition of an if / then /else
+####  - The command must return 0 on success
+####  - The command must return an exit code different from 0 on failure
+####  - The datafiles are stored in the same directory than the test script
+####  - The test script directory is stored in the TEST_DIR variable
+####  - If result files have to be produced they must be stored
+####    in the temporary directory (TMPDIR variable)
+####
+#### then clause is executed on success of the command
+####  - Write a success message using the log function
+####  - increment the variable success
+####
+#### else clause is executed on failure of the command
+####  - Write a failure message using the log function
+####  - increment the variable failed
+####
+######################################################################
+
+
+
+((ntest++))
+if $CMD -h > "${TMPDIR}/help.txt" 2>&1
+then
+    log "$MCMD: printing help OK"
+    ((success++))
+else
+    log "$MCMD: printing help failed"
+    ((failed++))
+fi
+
+
+#
+# Dataset used by the following tests: two families with a rare variant each,
+# a duplicate, and a sequence with an ambiguous nucleotide that is discarded.
+#
+cat > "${TMPDIR}/data.fasta" <<DATA
+>a1 count=20;
+acgtacgtacgtaacctagcctagcctagggatcgatcgatcgatcgaatcg
+>a2 count=3;
+acgtacgtacgtaacctagcctagcctagggatcgatcgatcgttcgaatcg
+>a3 count=2;
+acgtacgtacgtaacctagcctagcctagggatcgatcgatcgatcgaatcg
+>b1 count=15;
+ttgcatgcatgctagctagctagcatgcatcgatcgatgctagctagtagct
+>b2 count=1;
+ttgcatgcatgctagctagctagcatgcatcgatcgatgctagctagtaact
+>x1 count=4;
+ttgcatgcatgctangctagctagcatgcatcgatcgatgctagctagtagc
+DATA
+
+((ntest++))
+if $CMD --max-cpu 2 -O -t 0.95 "${TMPDIR}/data.fasta" > "${TMPDIR}/clusters.fasta" 2> "${TMPDIR}/clusters.log"
+then
+    log "$MCMD: clustering runs OK"
+    ((success++))
+else
+    log "$MCMD: clustering failed"
+    ((failed++))
+fi
+
+((ntest++))
+if [ "$(grep -c '^>' "${TMPDIR}/clusters.fasta")" = "5" ]
+then
+    log "$MCMD: the sequence with an ambiguous nucleotide is discarded OK"
+    ((success++))
+else
+    log "$MCMD: wrong number of sequences in the output"
+    ((failed++))
+fi
+
+((ntest++))
+if [ "$(grep '^>a[23] ' "${TMPDIR}/clusters.fasta" | grep -c 'cluster=a1;')" = "2" ] &&
+   [ "$(grep '^>b2 ' "${TMPDIR}/clusters.fasta" | grep -c 'cluster=b1;')" = "1" ] &&
+   grep '^>b1 ' "${TMPDIR}/clusters.fasta" | grep -q 'cluster_center=true;' &&
+   grep '^>a1 ' "${TMPDIR}/clusters.fasta" | grep -q 'cluster_weight=25;'
+then
+    log "$MCMD: sequences are attached to the right center OK"
+    ((success++))
+else
+    log "$MCMD: sequences are not attached to the right center"
+    ((failed++))
+fi
+
+((ntest++))
+if $CMD --max-cpu 2 -t 0.95 --otu-map "${TMPDIR}/otu.csv" --no-sequence-output "${TMPDIR}/data.fasta" > "${TMPDIR}/none.fasta" 2> /dev/null &&
+   [ ! -s "${TMPDIR}/none.fasta" ] &&
+   [ "$(head -n 1 "${TMPDIR}/otu.csv")" = "id,cluster,cluster_center,cluster_score,count" ] &&
+   [ "$(sed -n 2,4p "${TMPDIR}/otu.csv" | cut -d, -f1,2 | tr '\n' ' ')" = "a1,a1 a3,a1 a2,a1 " ] &&
+   [ "$(grep -c ',true,' "${TMPDIR}/otu.csv")" = "2" ]
+then
+    log "$MCMD: CSV table of the clusters OK"
+    ((success++))
+else
+    log "$MCMD: CSV table of the clusters failed"
+    ((failed++))
+fi
+
+((ntest++))
+if $CMD --max-cpu 1 -O -t 0.95 "${TMPDIR}/data.fasta" 2> /dev/null | grep '^>' | sed 's/ .*//' > "${TMPDIR}/order1.txt" &&
+   $CMD --max-cpu 8 -O -t 0.95 "${TMPDIR}/data.fasta" 2> /dev/null | grep '^>' | sed 's/ .*//' > "${TMPDIR}/order8.txt" &&
+   cmp -s "${TMPDIR}/order1.txt" "${TMPDIR}/order8.txt"
+then
+    log "$MCMD: the result does not depend on the number of threads OK"
+    ((success++))
+else
+    log "$MCMD: the result depends on the number of threads"
+    ((failed++))
+fi
+
+
+#########################################
+#
+# At the end of the tests
+# the cleanup function is called
+#
+#########################################
+
+cleanup

pkg/obialign/lcsband.go

@@ -40,7 +40,10 @@ const (
 type bandedLCSWorkspace struct {
 	aRev, bCode []uint32    // encoded bases (aRev is reversed), SIMD kernel only
 	rows        [3][]uint32 // antidiagonal (SIMD) or row (scalar) buffers
-	widened     int         // number of alignments that needed a second pass
+	aRev16      []uint16    // 16-bit encoded bases of the score-only kernel
+	bCode16     []uint16
+	rows16      [3][]uint16
+	widened     int // number of alignments that needed a second pass
 }
 
 var bandedLCSPool = sync.Pool{New: func() any { return new(bandedLCSWorkspace) }}
@@ -146,13 +149,7 @@ func bandedLCS(a, b []byte, maxError int, ws *bandedLCSWorkspace, useSIMD bool)
 	}
 	run := func(g int) (int, int) {
 		kmin, kmax := bandOffsets(lA, lB, g)
-		var key uint32
-		if simdOK {
-			key = bandedLCSSIMD(lA, lB, kmin, kmax, ws)
-		} else {
-			key = bandedLCSScalar(a, b, kmin, kmax, ws)
-		}
-		return int(key >> 16), int(lcsLenBase - key&0xFFFF)
+		return ws.align(a, b, kmin, kmax, simdOK)
 	}
 
 	if maxError < 0 {
@@ -173,3 +170,16 @@ func bandedLCS(a, b []byte, maxError int, ws *bandedLCSWorkspace, useSIMD bool)
 	}
 	return lcs, alilen
 }
+
+// align runs the banded DP on the offsets [kmin, kmax] (kmin <= 0 <= kmax) and
+// returns the best (lcs, alilen) of the band. The bases must have been encoded
+// with encodeBases when simdOK is set.
+func (ws *bandedLCSWorkspace) align(a, b []byte, kmin, kmax int, simdOK bool) (int, int) {
+	var key uint32
+	if simdOK {
+		key = bandedLCSSIMD(len(a), len(b), kmin, kmax, ws)
+	} else {
+		key = bandedLCSScalar(a, b, kmin, kmax, ws)
+	}
+	return int(key >> 16), int(lcsLenBase - key&0xFFFF)
+}

pkg/obialign/lcsband_nosimd.go

@@ -11,3 +11,7 @@ func encodeBases(ws *bandedLCSWorkspace, a, b []byte) {}
 func bandedLCSSIMD(lA, lB, kmin, kmax int, ws *bandedLCSWorkspace) uint32 {
 	return 0
 }
+
+func lcsScoreSIMD(a, b []byte, kmin, kmax, minLCS int, ws *bandedLCSWorkspace) int {
+	return -1
+}

pkg/obialign/lcsband_test.go

@@ -286,3 +286,75 @@ func TestFastLCSScoreWrapper(t *testing.T) {
 		t.Errorf("got (%d,%d), want (-1,-1)", s, l)
 	}
 }
+
+// TestBandedLCSAtLeast checks the exactness of the bound expressed on the
+// score: the optimum when it reaches minLCS, (-1,-1) otherwise.
+func TestBandedLCSAtLeast(t *testing.T) {
+	rng := rand.New(rand.NewSource(13))
+	var buf BandedLCSBuffer
+	for _, alpha := range testAlphabets {
+		for it := 0; it < 1500; it++ {
+			a := randomFrom(rng, alpha.letters, 1+rng.Intn(100))
+			b := mutateFrom(rng, alpha.letters, a, rng.Float64()*0.5)
+			if len(b) == 0 {
+				continue
+			}
+			os, ol := fullDP(a, b)
+			for _, minLCS := range []int{-3, 0, 1, os - 1, os, os + 1, len(b) / 2, len(b), len(b) + 1} {
+				ws, wl := os, ol
+				if os < minLCS {
+					ws, wl = -1, -1
+				}
+				for _, got := range [][2]int{func() [2]int { s, l, _ := buf.AtLeast(a, b, minLCS); return [2]int{s, l} }(),
+					func() [2]int { s, l, _ := BandedLCSAtLeast(b, a, minLCS); return [2]int{s, l} }()} {
+					if got[0] != ws || got[1] != wl {
+						t.Fatalf("%s minLCS=%d a=%q b=%q: got (%d,%d), want (%d,%d)",
+							alpha.name, minLCS, a, b, got[0], got[1], ws, wl)
+					}
+				}
+			}
+		}
+	}
+	if _, _, err := buf.AtLeast(make([]byte, MaxBandedLCSLength+1), []byte("a"), 0); err != ErrSequenceTooLong {
+		t.Errorf("too long: err = %v", err)
+	}
+}
+
+// TestBandedLCSScoreAtLeast checks the score-only entry point, with sequences
+// long enough for the early stop of the kernel to be exercised.
+func TestBandedLCSScoreAtLeast(t *testing.T) {
+	rng := rand.New(rand.NewSource(17))
+	var buf BandedLCSBuffer
+	check := func(name string, a, b []byte) {
+		os, _ := fullDP(a, b)
+		for _, minLCS := range []int{-1, 0, os - 3, os - 1, os, os + 1, os + 5, len(b) - 1, len(b), (len(b) * 9) / 10, len(b) + 1} {
+			want := os
+			if os < minLCS {
+				want = -1
+			}
+			got, err := buf.ScoreAtLeast(a, b, minLCS)
+			if err != nil || got != want {
+				t.Fatalf("%s minLCS=%d a=%q b=%q: got %d (%v), want %d", name, minLCS, a, b, got, err, want)
+			}
+		}
+	}
+	for _, alpha := range testAlphabets {
+		for it := 0; it < 800; it++ {
+			a := randomFrom(rng, alpha.letters, 1+rng.Intn(60))
+			b := mutateFrom(rng, alpha.letters, a, rng.Float64()*0.6)
+			if len(b) > 0 {
+				check(alpha.name, a, b)
+			}
+		}
+	}
+	for it := 0; it < 150; it++ {
+		a := randomFrom(rng, "ACGT", 100+rng.Intn(400))
+		b := mutateFrom(rng, "ACGT", a, rng.Float64()*0.3)
+		if it%3 == 0 {
+			b = randomFrom(rng, "ACGT", 50+rng.Intn(300))
+		}
+		if len(b) > 0 {
+			check("long", a, b)
+		}
+	}
+}

pkg/obialign/lcsmin.go

@@ -0,0 +1,102 @@
+package obialign
+
+// BandedLCSBuffer is a working memory that can be reused from one alignment to
+// the next to avoid any allocation. It must not be shared between goroutines.
+type BandedLCSBuffer struct {
+	ws bandedLCSWorkspace
+}
+
+// AtLeast is BandedLCSAtLeast on the buffer.
+func (b *BandedLCSBuffer) AtLeast(seqA, seqB []byte, minLCS int) (lcs, alilen int, err error) {
+	return atLeast(seqA, seqB, minLCS, &b.ws)
+}
+
+func atLeast(seqA, seqB []byte, minLCS int, ws *bandedLCSWorkspace) (lcs, alilen int, err error) {
+	if len(seqA) > MaxBandedLCSLength || len(seqB) > MaxBandedLCSLength {
+		return -1, -1, ErrSequenceTooLong
+	}
+	if len(seqA) < len(seqB) {
+		seqA, seqB = seqB, seqA
+	}
+	lcs, alilen = bandedLCSAtLeast(seqA, seqB, minLCS, ws, haveSIMD)
+	return lcs, alilen, nil
+}
+
+// BandedLCSAtLeast computes the LCS score of two nucleotide sequences and the
+// length of the shortest alignment achieving it, as BandedLCS does, but with
+// the bound expressed on the score: the result is the exact optimum when its
+// score is at least minLCS, and (-1, -1) otherwise.
+//
+// The DP only visits the diagonals an alignment of score minLCS can use (one
+// whose path makes at most lB-minLCS gaps on one side and lA-minLCS on the
+// other), so the cost decreases as minLCS grows. This is exact: every alignment
+// of score >= minLCS lies in that band, hence so does the optimum when it
+// reaches minLCS, and when the best path of the band is below minLCS so is
+// the global optimum.
+func BandedLCSAtLeast(seqA, seqB []byte, minLCS int) (lcs, alilen int, err error) {
+	ws := bandedLCSPool.Get().(*bandedLCSWorkspace)
+	lcs, alilen, err = atLeast(seqA, seqB, minLCS, ws)
+	bandedLCSPool.Put(ws)
+	return lcs, alilen, err
+}
+
+// bandedLCSAtLeast expects len(a) >= len(b), both within MaxBandedLCSLength.
+func bandedLCSAtLeast(a, b []byte, minLCS int, ws *bandedLCSWorkspace, useSIMD bool) (int, int) {
+	lA, lB := len(a), len(b)
+	minLCS = max(minLCS, 0)
+	if minLCS > lB {
+		return -1, -1
+	}
+	if lB == 0 {
+		return 0, lA
+	}
+	simdOK := useSIMD && allRegularIUPAC(a) && allRegularIUPAC(b)
+	kmin, kmax := -(lB - minLCS), lA-minLCS
+
+	if !simdOK {
+		lcs, alilen := ws.align(a, b, kmin, kmax, false)
+		if lcs < minLCS {
+			return -1, -1
+		}
+		return lcs, alilen
+	}
+
+	// The score alone is much cheaper than the score with the length of the
+	// alignment: the latter is only computed when the pair reaches minLCS.
+	if lcsScoreSIMD(a, b, kmin, kmax, minLCS, ws) < minLCS {
+		return -1, -1
+	}
+	encodeBases(ws, a, b)
+	return ws.align(a, b, kmin, kmax, true)
+}
+
+// ScoreAtLeast computes the LCS score of two nucleotide sequences when it is
+// at least minLCS, and returns -1 otherwise. It is much cheaper than AtLeast,
+// which also computes the length of the shortest alignment.
+func (b *BandedLCSBuffer) ScoreAtLeast(seqA, seqB []byte, minLCS int) (int, error) {
+	if len(seqA) > MaxBandedLCSLength || len(seqB) > MaxBandedLCSLength {
+		return -1, ErrSequenceTooLong
+	}
+	if len(seqA) < len(seqB) {
+		seqA, seqB = seqB, seqA
+	}
+	lA, lB := len(seqA), len(seqB)
+	minLCS = max(minLCS, 0)
+	if minLCS > lB {
+		return -1, nil
+	}
+	if lB == 0 {
+		return 0, nil
+	}
+	kmin, kmax := -(lB - minLCS), lA-minLCS
+	var lcs int
+	if haveSIMD && allRegularIUPAC(seqA) && allRegularIUPAC(seqB) {
+		lcs = lcsScoreSIMD(seqA, seqB, kmin, kmax, minLCS, &b.ws)
+	} else {
+		lcs, _ = b.ws.align(seqA, seqB, kmin, kmax, false)
+	}
+	if lcs < minLCS {
+		return -1, nil
+	}
+	return lcs, nil
+}

pkg/obialign/lcsscore_simd.go

@@ -0,0 +1,156 @@
+//go:build goexperiment.simd
+
+package obialign
+
+import "simd"
+
+func simdLanes16() int {
+	var probe simd.Uint16s
+	return probe.Len()
+}
+
+func growUint16(s []uint16, n int) []uint16 {
+	if cap(s) < n {
+		return make([]uint16, n)
+	}
+	return s[:n]
+}
+
+func encodeIUPAC16(dst []uint16, s []byte, rev bool) {
+	n := len(s)
+	clear(dst)
+	if rev {
+		for x, c := range s {
+			dst[n-1-x] = uint16(iupacMask[c])
+		}
+		return
+	}
+	for x, c := range s {
+		dst[x] = uint16(iupacMask[c])
+	}
+}
+
+// pruneEvery is the number of antidiagonals between two tests of the upper
+// bound that stops a hopeless alignment.
+const pruneEvery = 8
+
+// lcsScoreSIMD runs the same banded DP as bandedLCSSIMD on the score only,
+// with 16-bit lanes (twice the cells per instruction):
+//
+//	cell(i,j) = max(diag + match, up, left)
+//
+// A cell outside the band is 0, which never beats a real cell. The score of a
+// path ending at the cell (i, j) of an antidiagonal cannot exceed the score of
+// the cell plus min(lB-i, lA-j), the characters left to pair. Every path
+// crosses each antidiagonal inside the window, so when the best score of the
+// window plus the largest of these remainders is under minLCS the final score
+// is under minLCS: -1 is returned without computing the rest of the matrix.
+//
+// Requires lA >= lB >= 1, kmin <= 0 <= kmax, and bases with non-zero masks.
+// Returns the best score of the band, or -1 if it is proven to be under
+// minLCS.
+func lcsScoreSIMD(a, b []byte, kmin, kmax, minLCS int, ws *bandedLCSWorkspace) int {
+	lA, lB := len(a), len(b)
+	vl := simdLanes16()
+
+	ws.aRev16 = growUint16(ws.aRev16, lA+vl)
+	ws.bCode16 = growUint16(ws.bCode16, lB+vl)
+	encodeIUPAC16(ws.aRev16, a, true)
+	encodeIUPAC16(ws.bCode16, b, false)
+	aRev, bCode := ws.aRev16, ws.bCode16
+
+	size := lB + 2*vl + 2
+	for r := range ws.rows16 {
+		ws.rows16[r] = growUint16(ws.rows16[r], size)
+		clear(ws.rows16[r])
+	}
+	p2, p1, cur := ws.rows16[0], ws.rows16[1], ws.rows16[2]
+
+	// the first row and the first column hold a score of 0: nothing to set
+
+	zero := simd.BroadcastUint16s(0)
+	one := simd.BroadcastUint16s(1)
+
+	for t := 2; t <= lA+lB; t++ {
+		lo := max(1, t-lA, (t-kmax+1)>>1)
+		hi := min(lB, t-1, (t-kmin)>>1)
+
+		for i := lo; i <= hi; i += vl {
+			ca := simd.LoadUint16s(aRev[lA-t+i:])
+			cb := simd.LoadUint16s(bCode[i-1:])
+			inc := one.Masked(ca.And(cb).NotEqual(zero))
+			d := simd.LoadUint16s(p2[i-1:]).Add(inc)
+			u := simd.LoadUint16s(p1[i-1:])
+			l := simd.LoadUint16s(p1[i:])
+			d.Max(u).Max(l).Store(cur[i:])
+		}
+
+		zero.Store(cur[hi+1:])
+		if lo > 1 {
+			cur[lo-1] = 0
+		}
+
+		// A diagonal move skips an antidiagonal, but a path always visits
+		// one of two consecutive antidiagonals.
+		if t%pruneEvery == 0 && minLCS > 0 &&
+			scoreBound(p1, t-1, lA, lB, kmin, kmax) < minLCS &&
+			scoreBound(cur, t, lA, lB, kmin, kmax) < minLCS {
+			return -1
+		}
+
+		p2, p1, cur = p1, cur, p2
+	}
+	return int(p1[lB])
+}
+
+// iota16 is 0, 1, 2... to build the row index of the lanes.
+var iota16 = func() (t [64]uint16) {
+	for i := range t {
+		t[i] = uint16(i)
+	}
+	return t
+}()
+
+// scoreBound is an upper bound of the final score of the paths going through
+// the antidiagonal t, whose scores are in row. A path through the cell (i, j)
+// scores at most the score of the cell plus min(lB-i, lA-j), the characters
+// left to pair, so the bound is the maximum of this sum on the cells of the
+// window. The sum is computed by vectors on the full chunks of the window.
+func scoreBound(row []uint16, t, lA, lB, kmin, kmax int) int {
+	lo := max(1, t-lA, (t-kmax+1)>>1)
+	hi := min(lB, t-1, (t-kmin)>>1)
+
+	bound := 0
+	i := lo
+	if hi-lo >= simdLanes16() {
+		vl := simdLanes16()
+		idx := simd.LoadUint16s(iota16[:]).Add(simd.BroadcastUint16s(uint16(lo)))
+		step := simd.BroadcastUint16s(uint16(vl))
+		remB := simd.BroadcastUint16s(uint16(lB))
+		// lA-t+i is not negative on the window; the 16-bit arithmetic is modular
+		offA := simd.BroadcastUint16s(uint16(lA - t))
+		acc := simd.BroadcastUint16s(0)
+		for ; i+vl-1 <= hi; i += vl {
+			left := remB.Sub(idx).Min(idx.Add(offA))
+			acc = acc.Max(simd.LoadUint16s(row[i:]).Add(left))
+			idx = idx.Add(step)
+		}
+		var lanes [64]uint16
+		acc.Store(lanes[:])
+		for _, v := range lanes[:vl] {
+			bound = max(bound, int(v))
+		}
+	}
+	for ; i <= hi; i++ {
+		bound = max(bound, int(row[i])+min(lB-i, lA-t+i))
+	}
+
+	// the paths running along the first row or the first column have a score of 0
+	if t <= lA && t <= kmax {
+		bound = max(bound, min(lB, lA-t))
+	}
+	if t <= lB && -t >= kmin {
+		bound = max(bound, min(lB-t, lA))
+	}
+	return bound
+}

pkg/obitools/obiclust/block.go

@@ -0,0 +1,46 @@
+package obiclust
+
+// A block stores the 4-mer tables of a few centers, transposed: the counter
+// of the word w for the lane j is data[w*width+j]. A vector instruction then
+// handles the same word for all the centers of the block, and only the words
+// that a sequence contains (a hundred for a short amplicon, out of 256) need
+// to be visited to compare it with all the centers of the block.
+type tableBlock struct {
+	data []uint8
+}
+
+func newTableBlock(width int) tableBlock {
+	return tableBlock{data: make([]uint8, 256*width)}
+}
+
+// set stores the table t as the lane `lane` of the block.
+func (b *tableBlock) set(width, lane int, t *table4) {
+	for w := range t.count {
+		b.data[w*width+lane] = t.count[w]
+	}
+}
+
+// common computes the sums of the minima of the counters of the sequence
+// given by its words with every lane of the block (see blockCommon).
+func (b *tableBlock) common(width int, words []uint16, out []uint8) {
+	blockCommon(b.data, width, words, out)
+}
+
+// sparseWords lists the words of a table as w<<8|count, so that the visit of
+// a block only goes through the words present in the sequence. nil is
+// returned when the counters add up to more than 255, which would overflow the
+// 8-bit sums of the blocks.
+func sparseWords(t *table4) []uint16 {
+	words := make([]uint16, 0, 128)
+	mass := 0
+	for w, c := range t.count {
+		if c > 0 {
+			words = append(words, uint16(w)<<8|uint16(c))
+			mass += int(c)
+		}
+	}
+	if mass > 255 {
+		return nil
+	}
+	return words
+}

pkg/obitools/obiclust/block_nosimd.go

@@ -0,0 +1,10 @@
+//go:build !goexperiment.simd
+
+package obiclust
+
+// simdBlockWidth is 0 without SIMD: the blocks are not used.
+func simdBlockWidth() int { return 0 }
+
+func blockCommon(data []uint8, width int, words []uint16, out []uint8) {
+	panic("obiclust: blocks of tables require GOEXPERIMENT=simd")
+}

pkg/obitools/obiclust/block_simd.go

@@ -0,0 +1,25 @@
+//go:build goexperiment.simd
+
+package obiclust
+
+import "simd"
+
+// simdBlockWidth is the number of centers in a block: one per lane of a
+// vector of bytes.
+func simdBlockWidth() int {
+	var probe simd.Uint8s
+	return min(probe.Len(), 64)
+}
+
+// blockCommon computes, for the sequence whose words are given, the sum of
+// the minima of the counters with every lane of the block. It is the value of
+// commonWords without the overflow term, as the sums fit in 8 bits (see
+// sparseWords). out must hold at least `width` bytes.
+func blockCommon(data []uint8, width int, words []uint16, out []uint8) {
+	acc := simd.BroadcastUint8s(0)
+	for _, e := range words {
+		w := simd.LoadUint8s(data[int(e>>8)*width:])
+		acc = acc.Add(w.Min(simd.BroadcastUint8s(uint8(e))))
+	}
+	acc.Store(out)
+}

pkg/obitools/obiclust/centers.go

@@ -0,0 +1,136 @@
+package obiclust
+
+import (
+	"math"
+	"sort"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obialign"
+)
+
+// center is a copy of the entry of a center, with its own table: scanning
+// the centers of a list then reads contiguous memory.
+type center struct {
+	entry
+	idx  int // index of the entry in the dataset
+	rank int // rank of the center in the order of creation
+}
+
+const tabChunk = 1024
+
+// A bucket holds the centers of one length, in the order of creation, and
+// their tables by blocks (see tableBlock).
+type bucket struct {
+	cents  []center
+	blocks []tableBlock
+}
+
+// centerSet stores the centers by length. A sequence can only be attached to a
+// center whose length is compatible with its own (see lengthCompatible), so
+// it only visits the buckets of these lengths, instead of all the centers.
+type centerSet struct {
+	width int // centers per block of transposed tables, 0 if unused
+	byLen map[int]*bucket
+	lens  []int      // lengths that have a bucket, increasing
+	tabs  [][]table4 // chunks holding the tables of the centers
+	n     int
+}
+
+func newCenterSet(width int) *centerSet {
+	return &centerSet{width: width, byLen: make(map[int]*bucket)}
+}
+
+// add stores a copy of the entry e, which is the entry idx of the dataset, as
+// the next center, and returns it.
+func (s *centerSet) add(e entry, idx int) center {
+	if s.n%tabChunk == 0 {
+		s.tabs = append(s.tabs, make([]table4, tabChunk))
+	}
+	tab := &s.tabs[len(s.tabs)-1][s.n%tabChunk]
+	if e.table != nil {
+		*tab = *e.table
+	}
+	e.table = tab
+
+	b := s.byLen[e.length]
+	if b == nil {
+		b = new(bucket)
+		s.byLen[e.length] = b
+		s.lens = append(s.lens, e.length)
+		sort.Ints(s.lens)
+	}
+	if w := s.width; w > 0 && e.table != nil {
+		if len(b.cents)%w == 0 {
+			b.blocks = append(b.blocks, newTableBlock(w))
+		}
+		b.blocks[len(b.blocks)-1].set(w, len(b.cents)%w, tab)
+	}
+
+	ctr := center{entry: e, idx: idx, rank: s.n}
+	b.cents = append(b.cents, ctr)
+	s.n++
+	return ctr
+}
+
+// scan compares entry i with all the centers of the set, and returns the
+// first one it matches (in fast mode) or the best one (in exact mode, the
+// first of them in case of tie), exactly as compare would on the list of the
+// centers in the order of creation.
+//
+// Only the buckets of compatible lengths are visited: the other centers would
+// give the worst score. In each bucket the first match is the one of lowest
+// rank, so the first match of the whole set is the one of lowest rank among
+// the buckets. In exact mode, the best of each bucket is compared, ties going
+// to the lowest rank.
+func (c *clustering) scan(i int, buf *obialign.BandedLCSBuffer) attachment {
+	q := &c.entries[i]
+	set := c.set
+	width := set.width
+	useBlocks := width > 0 && q.sparse != nil
+
+	best := attachment{-1, c.sc.worst}
+	bestRank := math.MaxInt
+	var common [64]uint8
+
+	for _, length := range set.lens {
+		if !c.sc.lengthCompatible(q.length, length) {
+			continue
+		}
+		b := set.byLen[length]
+		local := attachment{-1, c.sc.worst}
+		localRank := 0
+
+		for k := range b.cents {
+			ctr := &b.cents[k]
+			if c.fast && ctr.rank > bestRank {
+				break // a center of lower rank has been found in another bucket
+			}
+			cw := -1
+			if useBlocks {
+				if k%width == 0 {
+					b.blocks[k/width].common(width, q.sparse, common[:])
+				}
+				cw = int(common[k%width])
+			}
+			s := c.sc.pairScore(q, &ctr.entry, cw, buf)
+			if c.sc.selects(s, local.score) {
+				local, localRank = attachment{ctr.idx, s}, ctr.rank
+				if c.fast {
+					break
+				}
+			}
+		}
+
+		if local.center < 0 {
+			continue
+		}
+		if c.fast {
+			if localRank < bestRank {
+				best, bestRank = local, localRank
+			}
+		} else if best.center < 0 || c.sc.beats(local.score, best.score) ||
+			(local.score == best.score && localRank < bestRank) {
+			best, bestRank = local, localRank
+		}
+	}
+	return best
+}

pkg/obitools/obiclust/cluster.go

@@ -0,0 +1,202 @@
+package obiclust
+
+import (
+	"sort"
+	"sync"
+	"sync/atomic"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obialign"
+)
+
+// clustering is the state of the star clustering of the distinct sequences,
+// taken in their sorted order.
+//
+// The reference algorithm is sequential: each sequence is compared with the
+// centers created so far, in the order of their creation, and is attached to
+// the first one it matches (or to the best one in exact mode), or becomes a
+// new center. Its result is reproduced exactly while the comparisons are run
+// in parallel, by processing the sequences by blocks:
+//
+//   - phase A (parallel): every sequence of the block is compared with the
+//     centers existing when the block starts. This is independent from one
+//     sequence to the other, a sequence of the block cannot change the centers;
+//   - phase B (sequential): the sequences matching no center are then taken
+//     in their order. Each one is compared with the centers created earlier in
+//     the block, and becomes a new center if it still matches nothing. The
+//     new centers come after the old ones in the order of the centers, so
+//     the result is the one of the sequential algorithm;
+//   - phase C (parallel, exact mode only): the sequences attached in phase A
+//     are compared with the new centers that precede them, the best score of
+//     the whole list of centers being searched for.
+//
+// The result does not depend on the size of the blocks, which only trades the
+// sequential work of phase B against the synchronizations.
+type clustering struct {
+	entries []entry
+	sc      *scoring
+	fast    bool
+	workers int
+	// bounds of the size of the blocks, 0 for the defaults (tests only)
+	blockMin, blockMax int
+
+	centers []int // indices of the centers, in the order of creation
+	set     *centerSet
+	fresh   []center // the centers created in the current block
+
+	center []int     // for each entry, the index of its center, -1 if it has none
+	score  []float64 // for each entry, the score with its center
+	bufs   []obialign.BandedLCSBuffer
+}
+
+// result of the comparison of one entry with the list of centers
+type attachment struct {
+	center int // index of the center, -1 if none
+	score  float64
+}
+
+func newClustering(entries []entry, sc *scoring, fast bool, workers int) *clustering {
+	c := &clustering{
+		entries: entries,
+		sc:      sc,
+		fast:    fast,
+		workers: max(workers, 1),
+		center:  make([]int, len(entries)),
+		score:   make([]float64, len(entries)),
+		bufs:    make([]obialign.BandedLCSBuffer, max(workers, 1)),
+	}
+	for i := range c.center {
+		c.center[i] = -1
+	}
+	c.set = newCenterSet(simdBlockWidth())
+	return c
+}
+
+func (c *clustering) addCenter(i int) {
+	c.fresh = append(c.fresh, c.set.add(c.entries[i], i))
+	c.centers = append(c.centers, i)
+	c.center[i] = i
+	c.score[i] = c.sc.centerScore(c.entries[i].length)
+}
+
+// compare looks for the best center of entry i among the given ones. The
+// attachment `from` is the best one already known. The search stops at the
+// first match in fast mode.
+func (c *clustering) compare(i int, cents []center, from attachment, buf *obialign.BandedLCSBuffer) attachment {
+	best := from
+	for k := range cents {
+		s := c.sc.pairScore(&c.entries[i], &cents[k].entry, -1, buf)
+		if c.sc.selects(s, best.score) {
+			best = attachment{cents[k].idx, s}
+			if c.fast {
+				break
+			}
+		}
+	}
+	return best
+}
+
+// parallelFor runs f(i, buf) for i in [from, to) on the workers.
+func (c *clustering) parallelFor(from, to int, f func(i int, buf *obialign.BandedLCSBuffer)) {
+	n := to - from
+	if c.workers == 1 || n == 1 {
+		for i := from; i < to; i++ {
+			f(i, &c.bufs[0])
+		}
+		return
+	}
+
+	var next atomic.Int64
+	next.Store(int64(from))
+	var wg sync.WaitGroup
+	for w := 0; w < min(c.workers, n); w++ {
+		wg.Add(1)
+		go func(buf *obialign.BandedLCSBuffer) {
+			defer wg.Done()
+			for {
+				i := int(next.Add(1)) - 1
+				if i >= to {
+					return
+				}
+				f(i, buf)
+			}
+		}(&c.bufs[w])
+	}
+	wg.Wait()
+}
+
+// run clusters all the entries. progress is called with the number of
+// entries processed.
+func (c *clustering) run(progress func(done int)) {
+	n := len(c.entries)
+	if n == 0 {
+		return
+	}
+
+	minBlock, maxBlock := 2*c.workers, 256*c.workers
+	if c.blockMax > 0 {
+		minBlock, maxBlock = c.blockMin, c.blockMax
+	}
+	block := minBlock
+	att := make([]attachment, maxBlock)
+	inA := make([]bool, maxBlock) // attached to a center existing before the block
+	var newCenters []int          // indices of the centers created in the block
+
+	for pos := 0; pos < n; {
+		end := min(n, pos+block)
+		c.fresh = c.fresh[:0]
+		att, inA := att[:end-pos], inA[:end-pos]
+
+		// phase A
+		c.parallelFor(pos, end, func(i int, buf *obialign.BandedLCSBuffer) {
+			att[i-pos] = c.scan(i, buf)
+			inA[i-pos] = att[i-pos].center >= 0
+		})
+
+		// phase B
+		unmatched := 0
+		newCenters = newCenters[:0]
+		for i := pos; i < end; i++ {
+			a := &att[i-pos]
+			if inA[i-pos] {
+				continue
+			}
+			unmatched++
+			*a = c.compare(i, c.fresh, *a, &c.bufs[0])
+			if a.center < 0 && !c.entries[i].ambiguous {
+				newCenters = append(newCenters, i)
+				c.addCenter(i)
+			}
+		}
+
+		// phase C
+		if !c.fast && len(newCenters) > 0 {
+			c.parallelFor(pos, end, func(i int, buf *obialign.BandedLCSBuffer) {
+				if inA[i-pos] {
+					before := c.fresh[:sort.SearchInts(newCenters, i)]
+					att[i-pos] = c.compare(i, before, att[i-pos], buf)
+				}
+			})
+		}
+
+		for i := pos; i < end; i++ {
+			if a := att[i-pos]; a.center >= 0 {
+				c.center[i] = a.center
+				c.score[i] = c.sc.memberScore(a.score)
+			}
+		}
+
+		// Size of the next block. Phase B is sequential: for a block of b
+		// sequences of which a fraction u matches no old center and a fraction
+		// n becomes new centers, it makes about b*u*b*n/2 comparisons, against
+		// b*K/workers in the time of phase A (K old centers). The block is
+		// sized so that phase B stays around a tenth of phase A.
+		if fu, fn := float64(unmatched)/float64(end-pos), float64(len(newCenters))/float64(end-pos); fu*fn > 0 {
+			target := 0.2 * float64(len(c.centers)) / (float64(c.workers) * fu * fn)
+			block = int(min(float64(maxBlock), max(float64(minBlock), target)))
+		} else {
+			block = maxBlock
+		}
+		pos = end
+		progress(pos)
+	}
+}

pkg/obitools/obiclust/kmer4.go

@@ -0,0 +1,47 @@
+package obiclust
+
+// table4 is the 4-mer occurrence table of a sequence, as sumaclust builds it:
+// one saturating counter per word, and the number of occurrences that did
+// not fit in the counters.
+type table4 struct {
+	count    [256]uint8
+	overflow int
+}
+
+// buildTable4 counts the 4-mers of a sequence made of the letters a, c, g
+// and t. The 2-bit code of a base is (letter>>1)&3, i.e. a=0, c=1, t=2, g=3,
+// which is the encoding of sumaclust.
+func buildTable4(seq []byte) *table4 {
+	t := new(table4)
+	t.fill(seq)
+	return t
+}
+
+// fill counts the 4-mers of seq in a zeroed table.
+func (t *table4) fill(seq []byte) {
+	if len(seq) < 4 {
+		return
+	}
+	w := uint(0)
+	for i, c := range seq {
+		w = (w<<2 | uint(c>>1)&3) & 0xFF
+		if i < 3 {
+			continue
+		}
+		if t.count[w] < 255 {
+			t.count[w]++
+		} else {
+			t.overflow++
+		}
+	}
+}
+
+// minCommonWords is the minimum number of 4-mers that two sequences must
+// share when the longest has length reflen and they have a common
+// subsequence of length lcs (integer arithmetic of sumaclust, thresholdLCS4).
+func minCommonWords(reflen, lcs int) int {
+	nbfrag := (reflen-lcs)*2 + 1
+	smin := lcs / nbfrag
+	r := lcs - smin*nbfrag
+	return max(smin-2, 0)*r + max(smin-3, 0)*(nbfrag-r)
+}

pkg/obitools/obiclust/kmer4_nosimd.go

@@ -0,0 +1,14 @@
+//go:build !goexperiment.simd
+
+package obiclust
+
+// commonWords is the upper bound sumaclust uses for the number of 4-mers
+// shared by two sequences: the sum of the minima of the counters, plus the
+// minimum of the two overflows.
+func commonWords(t1, t2 *table4) int {
+	total := 0
+	for i := range t1.count {
+		total += int(min(t1.count[i], t2.count[i]))
+	}
+	return total + min(t1.overflow, t2.overflow)
+}

pkg/obitools/obiclust/kmer4_simd.go

@@ -0,0 +1,35 @@
+//go:build goexperiment.simd
+
+package obiclust
+
+import "simd"
+
+// commonWords is the upper bound sumaclust uses for the number of 4-mers
+// shared by two sequences: the sum of the minima of the counters, plus the
+// minimum of the two overflows.
+//
+// The minima of the 256 counters are computed by vectors of bytes, and summed
+// in 16-bit lanes (at most 256*255 spread over the lanes, the lanes being at
+// least 8 in number, so that none of them overflows).
+func commonWords(t1, t2 *table4) int {
+	var probe simd.Uint8s
+	vl := probe.Len()
+
+	acc := simd.BroadcastUint16s(0)
+	low := simd.BroadcastUint16s(0x00FF)
+	for i := 0; i < len(t1.count); i += vl {
+		m := simd.LoadUint8s(t1.count[i:]).Min(simd.LoadUint8s(t2.count[i:])).ReshapeToUint16s()
+		acc = acc.Add(m.And(low)).Add(m.ShiftAllRight(8))
+	}
+
+	// sum the pairs of 16-bit lanes into 32-bit lanes, then add those up
+	wide := acc.ReshapeToUint32s()
+	sums := wide.And(simd.BroadcastUint32s(0xFFFF)).Add(wide.ShiftAllRight(16))
+	var lanes [32]uint32
+	sums.Store(lanes[:])
+	total := 0
+	for _, v := range lanes[:sums.Len()] {
+		total += int(v)
+	}
+	return total + min(t1.overflow, t2.overflow)
+}

pkg/obitools/obiclust/kmer4_test.go

@@ -0,0 +1,71 @@
+package obiclust
+
+import (
+	"math/rand"
+	"testing"
+)
+
+// commonWordsRef is the definition of commonWords, spelled out.
+func commonWordsRef(t1, t2 *table4) int {
+	total := 0
+	for i := range t1.count {
+		total += int(min(t1.count[i], t2.count[i]))
+	}
+	return total + min(t1.overflow, t2.overflow)
+}
+
+func TestCommonWords(t *testing.T) {
+	rng := rand.New(rand.NewSource(3))
+	seq := func(n int, alpha string) []byte {
+		s := make([]byte, n)
+		for i := range s {
+			s[i] = alpha[rng.Intn(len(alpha))]
+		}
+		return s
+	}
+	for it := 0; it < 3000; it++ {
+		alpha := []string{"acgt", "ac", "a"}[it%3]
+		t1 := buildTable4(seq(rng.Intn(1200), alpha))
+		t2 := buildTable4(seq(rng.Intn(1200), alpha))
+		if got, want := commonWords(t1, t2), commonWordsRef(t1, t2); got != want {
+			t.Fatalf("commonWords = %d, want %d", got, want)
+		}
+	}
+}
+
+// TestBuildTable4 checks the table against the 4-mers counted the long way,
+// including the saturation of the counters.
+func TestBuildTable4(t *testing.T) {
+	code := map[byte]int{'a': 0, 'c': 1, 't': 2, 'g': 3}
+	rng := rand.New(rand.NewSource(4))
+	for it := 0; it < 500; it++ {
+		alpha := []string{"acgt", "a", "ac"}[it%3]
+		n := rng.Intn(900)
+		s := make([]byte, n)
+		for i := range s {
+			s[i] = alpha[rng.Intn(len(alpha))]
+		}
+		var counts [256]int
+		for i := 0; i+4 <= n; i++ {
+			w := 0
+			for _, c := range s[i : i+4] {
+				w = w<<2 | code[c]
+			}
+			counts[w]++
+		}
+		tab := buildTable4(s)
+		over := 0
+		for w, c := range counts {
+			if c > 255 {
+				over += c - 255
+				c = 255
+			}
+			if int(tab.count[w]) != c {
+				t.Fatalf("word %d: got %d, want %d", w, tab.count[w], c)
+			}
+		}
+		if tab.overflow != over {
+			t.Fatalf("overflow = %d, want %d", tab.overflow, over)
+		}
+	}
+}

pkg/obitools/obiclust/obiclust.go

@@ -1 +1,225 @@
 package obiclust
+
+import (
+	"os"
+	"sync"
+	"sync/atomic"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obialign"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obicsv"
+	"github.com/schollz/progressbar/v3"
+	log "github.com/sirupsen/logrus"
+)
+
+// buildEntries describes the distinct sequences of the groups, the 4-mer
+// tables being computed in parallel.
+func buildEntries(recs []record, groups []group, workers int) []entry {
+	entries := make([]entry, len(groups))
+	tables := make([]table4, len(groups)) // contiguous, in the order the centers are scanned
+
+	var next atomic.Int64
+	var wg sync.WaitGroup
+	for w := 0; w < max(workers, 1); w++ {
+		wg.Add(1)
+		go func() {
+			defer wg.Done()
+			for {
+				g := int(next.Add(1)) - 1
+				if g >= len(groups) {
+					return
+				}
+				head := &recs[groups[g].start]
+				var sparse []uint16
+				if !head.ambiguous {
+					tables[g].fill(head.clean)
+					sparse = sparseWords(&tables[g])
+				}
+				entries[g] = entry{
+					seq:       head.clean,
+					length:    len(head.clean),
+					count:     groups[g].count,
+					table:     &tables[g],
+					sparse:    sparse,
+					ambiguous: head.ambiguous,
+				}
+			}
+		}()
+	}
+	wg.Wait()
+	return entries
+}
+
+// Params are the parameters of the clustering.
+type Params struct {
+	Threshold       float64
+	Ratio           float64
+	Exact           bool // attach a sequence to the best center, not to the first matching one
+	Distance        bool // the score is a distance, not a similarity
+	Normalized      bool // the score is normalized by the reference length
+	Reference       reference
+	SortKey         string // "count", "None", or an attribute
+	Ascending       bool
+	AcceptAmbiguous bool // keep the sequences with IUPAC letters other than acgt (they cannot be centers)
+	Workers         int
+}
+
+// ParamsFromCLI collects the parameters from the command line options.
+func ParamsFromCLI() Params {
+	return Params{
+		Threshold:       CLIThreshold(),
+		Ratio:           CLIRatio(),
+		Exact:           CLIExact(),
+		Distance:        CLIDistance(),
+		Normalized:      CLINormalized(),
+		Reference:       CLIReference(),
+		SortKey:         CLISortKey(),
+		Ascending:       CLIAscending(),
+		AcceptAmbiguous: CLIAcceptAmbiguous(),
+		Workers:         obidefault.ParallelWorkers(),
+	}
+}
+
+// newScoring builds the scoring from the parameters, checking them as sumaclust does.
+func newScoring(p Params, entries []entry) *scoring {
+	threshold := p.Threshold
+
+	if threshold <= 0 || (p.Normalized && threshold > 1.0) {
+		log.Fatal("Please specify a threshold > 0, and < 1 when scores are normalized.")
+	}
+
+	sc := &scoring{
+		normalize: p.Normalized,
+		lcsmode:   !p.Distance,
+		ref:       p.Reference,
+		ratio:     p.Ratio,
+	}
+	if !sc.lcsmode && sc.normalize {
+		threshold = 1.0 - threshold
+	}
+	sc.threshold = threshold
+
+	lmax := 0
+	for i := range entries {
+		lmax = max(lmax, entries[i].length)
+	}
+	if sc.similarityLike() {
+		sc.worst = 0.0
+	} else {
+		sc.worst = float64(lmax)
+	}
+	sc.prepareLengths(lmax)
+	return sc
+}
+
+func progressBar(n int) *progressbar.ProgressBar {
+	if !obiconvert.CLIProgressBar() {
+		return nil
+	}
+	return progressbar.NewOptions(n,
+		progressbar.OptionSetWriter(os.Stderr),
+		progressbar.OptionSetWidth(15),
+		progressbar.OptionShowIts(),
+		progressbar.OptionSetPredictTime(true),
+		progressbar.OptionSetDescription("[Clustering sequences]"),
+	)
+}
+
+// Result is a clustering of a dataset.
+type Result struct {
+	recs      []record
+	groups    []group
+	clustered *clustering
+	Discarded int // number of sequences that were not usable
+}
+
+// Clusters returns the number of clusters.
+func (r *Result) Clusters() int { return len(r.clustered.centers) }
+
+// Cluster clusters the sequences with the star clustering algorithm of
+// sumaclust (the same as UCLUST and CD-HIT). progress, if not nil, is called
+// with the number of distinct sequences processed.
+func Cluster(db obiseq.BioSequenceSlice, p Params, progress func(done, total int)) *Result {
+	recs, groups, discarded := prepare(db, p.SortKey, p.Ascending, p.AcceptAmbiguous)
+
+	if discarded > 0 {
+		log.Warnf("Discarded %d sequences that did not contain only IUPAC nucleotides (or only 'acgt' without --accept-ambiguous)", discarded)
+	}
+	if len(groups) == 0 {
+		log.Fatal("No valid sequences.")
+	}
+	log.Infof("%d distinct sequences", len(groups))
+
+	entries := buildEntries(recs, groups, p.Workers)
+	for i := range entries {
+		if entries[i].length > obialign.MaxBandedLCSLength {
+			log.Fatalf("The sequence %s is too long (%d bp, maximum %d bp)",
+				recs[groups[i].start].seq.Id(), entries[i].length, obialign.MaxBandedLCSLength)
+		}
+	}
+
+	sc := newScoring(p, entries)
+	if sc.similarityLike() {
+		log.Infof("Clustering sequences when similarity >= %f", sc.threshold)
+	} else {
+		log.Infof("Clustering sequences when distance <= %f", sc.threshold)
+	}
+
+	cl := newClustering(entries, sc, !p.Exact, p.Workers)
+	cl.run(func(done int) {
+		if progress != nil {
+			progress(done, len(entries))
+		}
+	})
+	log.Infof("%d clusters created", len(cl.centers))
+
+	return &Result{recs: recs, groups: groups, clustered: cl, Discarded: discarded}
+}
+
+// CLIOBIClust clusters the sequences and returns them annotated.
+func CLIOBIClust(iterator obiiter.IBioSequence) obiiter.IBioSequence {
+	source, db := iterator.Load()
+	log.Infof("Sequence dataset of %d sequences loaded", len(db))
+
+	var bar *progressbar.ProgressBar
+	last := 0
+	res := Cluster(db, ParamsFromCLI(), func(done, total int) {
+		if bar == nil {
+			bar = progressBar(total)
+		}
+		if bar != nil {
+			bar.Add(done - last)
+		}
+		last = done
+	})
+
+	if CLIOTUMap() != "" {
+		table, err := obicsv.WriteCSVToFile(
+			res.OTUMapIterator(source, obidefault.BatchSize()),
+			CLIOTUMap(),
+			obicsv.OptionsCompressed(obidefault.CompressOutput()))
+		if err != nil {
+			log.Fatalf("Cannot write the OTU map %s: %v", CLIOTUMap(), err)
+		}
+		table.Consume()
+	}
+
+	if CLINoSequenceOutput() {
+		return emptyIterator()
+	}
+	return obiiter.IBatchOver(source, res.Annotate(), obidefault.BatchSize())
+}
+
+// emptyIterator returns an iterator that is already exhausted.
+func emptyIterator() obiiter.IBioSequence {
+	iterator := obiiter.MakeIBioSequence()
+	iterator.Add(1)
+	go func() {
+		iterator.WaitAndClose()
+	}()
+	iterator.Done()
+	return iterator
+}

pkg/obitools/obiclust/obiclust_test.go

@@ -0,0 +1,434 @@
+package obiclust
+
+import (
+	"bufio"
+	"fmt"
+	"math/rand"
+	"os"
+	"path/filepath"
+	"strconv"
+	"strings"
+	"testing"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obialign"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
+)
+
+// readTestFasta reads a fasta file whose headers are "id count=N; key=V;".
+func readTestFasta(t testing.TB, filename string) obiseq.BioSequenceSlice {
+	t.Helper()
+	f, err := os.Open(filename)
+	if err != nil {
+		t.Fatal(err)
+	}
+	defer f.Close()
+
+	var db obiseq.BioSequenceSlice
+	var header string
+	var seq strings.Builder
+	flush := func() {
+		if header == "" {
+			return
+		}
+		fields := strings.Fields(header)
+		s := obiseq.NewBioSequence(fields[0], []byte(seq.String()), "")
+		for _, f := range fields[1:] {
+			if k, v, ok := strings.Cut(strings.TrimSuffix(f, ";"), "="); ok {
+				if n, err := strconv.Atoi(v); err == nil {
+					s.SetAttribute(k, n)
+				}
+			}
+		}
+		db = append(db, s)
+		seq.Reset()
+	}
+	sc := bufio.NewScanner(f)
+	sc.Buffer(make([]byte, 1<<20), 1<<20)
+	for sc.Scan() {
+		if line := sc.Text(); strings.HasPrefix(line, ">") {
+			flush()
+			header = line[1:]
+		} else {
+			seq.WriteString(strings.TrimSpace(line))
+		}
+	}
+	flush()
+	return db
+}
+
+// paramsFromSumaclust translates the options of sumaclust.
+func paramsFromSumaclust(t testing.TB, args []string) Params {
+	t.Helper()
+	p := Params{Threshold: 0.97, Ratio: 1.0, Normalized: true, SortKey: "count", Workers: 4}
+	for i := 0; i < len(args); i++ {
+		var err error
+		switch args[i] {
+		case "-t":
+			i++
+			p.Threshold, err = strconv.ParseFloat(args[i], 64)
+		case "-R":
+			i++
+			p.Ratio, err = strconv.ParseFloat(args[i], 64)
+		case "-s":
+			i++
+			p.SortKey = args[i]
+		case "-e":
+			p.Exact = true
+		case "-l":
+			p.Reference = refShortest
+		case "-L":
+			p.Reference = refLongest
+		case "-a":
+			p.Reference = refAlignment
+		case "-d":
+			p.Distance = true
+		case "-r":
+			p.Normalized = false
+		case "-o":
+			p.Ascending = true
+		case "-g":
+			p.AcceptAmbiguous = true
+		default:
+			t.Fatalf("unknown option %s", args[i])
+		}
+		if err != nil {
+			t.Fatal(err)
+		}
+	}
+	return p
+}
+
+// TestSumaclustResults compares the clusterings with the outputs of
+// sumaclust 1.0.36 (testdata/*.expected: id, cluster, score, center, weight
+// and sequence of every record, in the order sumaclust writes them).
+func TestSumaclustResults(t *testing.T) {
+	cases, err := os.ReadFile(filepath.Join("testdata", "cases.txt"))
+	if err != nil {
+		t.Fatal(err)
+	}
+	for _, line := range strings.Split(strings.TrimSpace(string(cases)), "\n") {
+		parts := strings.Split(line, "\t")
+		data, name, opts := parts[0], parts[1], strings.Fields(parts[2])
+		t.Run(data+"/"+name, func(t *testing.T) {
+			db := readTestFasta(t, filepath.Join("testdata", data+".fasta"))
+			res := Cluster(db, paramsFromSumaclust(t, opts), nil)
+
+			expected, err := os.ReadFile(filepath.Join("testdata", data+"_"+name+".expected"))
+			if err != nil {
+				t.Fatal(err)
+			}
+			want := strings.Split(strings.TrimSpace(string(expected)), "\n")
+			got := res.Annotate()
+			if len(got) != len(want) {
+				t.Fatalf("%d records, want %d", len(got), len(want))
+			}
+			for i, s := range got {
+				score, _ := s.GetFloatAttribute("cluster_score")
+				center, _ := s.GetBoolAttribute("cluster_center")
+				c := map[bool]string{true: "T", false: "F"}[center]
+				cluster, _ := s.GetStringAttribute("cluster")
+				weight, _ := s.GetIntAttribute("cluster_weight")
+				line := fmt.Sprintf("%s\t%s\t%f\t%s\t%d\t%s", s.Id(), cluster, score, c, weight, s.String())
+				if line != want[i] {
+					t.Fatalf("record %d:\n got %s\nwant %s", i, line, want[i])
+				}
+			}
+		})
+	}
+}
+
+// referenceCluster transcribes the sequential algorithm of sumaclust.
+func referenceCluster(entries []entry, sc *scoring, fast bool) (center []int, score []float64) {
+	n := len(entries)
+	center, score = make([]int, n), make([]float64, n)
+	var centers []int
+	var buf obialign.BandedLCSBuffer
+	for i := range entries {
+		scoremax, best := sc.worst, -1
+		for _, c := range centers {
+			s := sc.pairScore(&entries[i], &entries[c], -1, &buf)
+			if sc.selects(s, scoremax) {
+				scoremax, best = s, c
+				if fast {
+					break
+				}
+			}
+		}
+		if best >= 0 {
+			center[i], score[i] = best, sc.memberScore(scoremax)
+		} else if entries[i].ambiguous {
+			center[i] = -1
+		} else {
+			center[i], score[i] = i, sc.centerScore(entries[i].length)
+			centers = append(centers, i)
+		}
+	}
+	return center, score
+}
+
+func randomEntries(rng *rand.Rand, n int) []entry {
+	var roots [][]byte
+	entries := make([]entry, 0, n)
+	for len(entries) < n {
+		var s []byte
+		if len(roots) == 0 || rng.Intn(5) == 0 {
+			s = make([]byte, 30+rng.Intn(50))
+			for i := range s {
+				s[i] = "acgt"[rng.Intn(4)]
+			}
+			roots = append(roots, s)
+		} else {
+			root := roots[rng.Intn(len(roots))]
+			for _, c := range root {
+				switch r := rng.Intn(40); {
+				case r == 0:
+					s = append(s, "acgt"[rng.Intn(4)])
+				case r == 1:
+				case r == 2:
+					s = append(s, c, "acgt"[rng.Intn(4)])
+				default:
+					s = append(s, c)
+				}
+			}
+		}
+		tab := buildTable4(s)
+		entries = append(entries, entry{seq: s, length: len(s), count: 1 + rng.Intn(20), table: tab, sparse: sparseWords(tab)})
+	}
+	return entries
+}
+
+// TestParallelClusteringIsSequential checks that the clustering by blocks
+// gives, whatever the number of workers and the size of the blocks, the
+// result of the sequential algorithm.
+func TestParallelClusteringIsSequential(t *testing.T) {
+	rng := rand.New(rand.NewSource(21))
+	scorings := []scoring{
+		{threshold: 0.9, normalize: true, lcsmode: true, ref: refAlignment, ratio: 1, worst: 0},
+		{threshold: 0.85, normalize: true, lcsmode: true, ref: refShortest, ratio: 2, worst: 0},
+		{threshold: 0.9, normalize: true, lcsmode: false, ref: refLongest, ratio: 1, worst: 0},
+		{threshold: 35, normalize: false, lcsmode: true, ref: refAlignment, ratio: 1, worst: 0},
+		{threshold: 5, normalize: false, lcsmode: false, ref: refAlignment, ratio: 1, worst: 80},
+	}
+	for round := 0; round < 4; round++ {
+		entries := randomEntries(rng, 300)
+		for si := range scorings {
+			sc := scorings[si]
+			for _, fast := range []bool{true, false} {
+				wantCenter, wantScore := referenceCluster(entries, &sc, fast)
+				for _, workers := range []int{1, 3, 8} {
+					for _, blocks := range [][2]int{{0, 0}, {1, 1}, {2, 5}, {7, 7}, {50, 300}} {
+						cl := newClustering(entries, &sc, fast, workers)
+						cl.blockMin, cl.blockMax = blocks[0], blocks[1]
+						cl.run(func(int) {})
+						for i := range entries {
+							if cl.center[i] != wantCenter[i] || cl.score[i] != wantScore[i] {
+								t.Fatalf("scoring %d fast=%v workers=%d blocks=%v: entry %d is (%d, %v), want (%d, %v)",
+									si, fast, workers, blocks, i, cl.center[i], cl.score[i], wantCenter[i], wantScore[i])
+							}
+						}
+					}
+				}
+			}
+		}
+	}
+}
+
+func TestClassify(t *testing.T) {
+	cases := []struct {
+		in        string
+		accept    bool
+		kept      bool
+		ambiguous bool
+	}{
+		{"acgt", false, true, false}, {"acgt", true, true, false},
+		{"acgtn", false, false, false}, {"acgtn", true, true, true},
+		{"acgtx", true, false, false}, {"nacgt", false, false, false},
+		{"acgt-", true, false, false}, {"acgu", true, true, true},
+		{"ACGT", true, false, false}, {"", true, false, false},
+		{"rykmswbdhvn", true, true, true}, {"rykmswbdhvn", false, false, false},
+	}
+	for _, c := range cases {
+		got, amb := classify([]byte(c.in), c.accept)
+		if (got != nil) != c.kept || amb != c.ambiguous {
+			t.Errorf("classify(%q, %v) = (%q, %v), want kept=%v ambiguous=%v", c.in, c.accept, got, amb, c.kept, c.ambiguous)
+		}
+	}
+}
+
+func makeSeq(id, seq string, count int, key float64) *obiseq.BioSequence {
+	s := obiseq.NewBioSequence(id, []byte(seq), "")
+	s.SetAttribute("count", count)
+	s.SetAttribute("key", key)
+	return s
+}
+
+func ids(groups []group, recs []record) string {
+	var out []string
+	for _, g := range groups {
+		out = append(out, recs[g.start].seq.Id())
+	}
+	return strings.Join(out, " ")
+}
+
+// TestPrepareOrder checks the order of the sequences, which does not depend
+// on the stability of a sort: decreasing count, then position; the head of a
+// group of identical sequences is the one with the extreme key, then the
+// first one.
+func TestPrepareOrder(t *testing.T) {
+	db := obiseq.BioSequenceSlice{
+		makeSeq("a", "aaaacccc", 5, 1),
+		makeSeq("b", "gggg", 9, 2),
+		makeSeq("c", "aaaacccc", 5, 3), // same sequence as a, same count: a is the head
+		makeSeq("d", "tttt", 10, 4),
+		makeSeq("e", "cccc", 10, 5), // same cumulated count as d: after d, which comes first
+		makeSeq("f", "aaaacccc", 7, 6),
+		makeSeq("g", "nnnn", 3, 7), // discarded
+		makeSeq("h", "ccgg", 2, 8),
+	}
+
+	check := func(key string, ascending bool, want string) {
+		recs, groups, discarded := prepare(db, key, ascending, false)
+		if discarded != 1 {
+			t.Errorf("discarded = %d, want 1", discarded)
+		}
+		if got := ids(groups, recs); got != want {
+			t.Errorf("key=%s ascending=%v: got %s, want %s", key, ascending, got, want)
+		}
+	}
+	// a, c and f are one group of count 17, headed by f (count 7)
+	check("count", false, "f d e b h")
+	check("count", true, "h b d e a") // the head of a group is then the record with the smallest count
+	// on the key attribute, the groups are ranked on the key of their head, the record with the largest key
+	check("key", false, "h f e d b")
+	check("key", true, "a b d e h")
+	// no sorting: first occurrence of each sequence
+	check("None", false, "a b d e h")
+
+	// the identical sequences follow their head, with the largest count first
+	recs, groups, _ := prepare(db, "count", false, false)
+	var members []string
+	for r := groups[0].start; r < groups[0].end; r++ {
+		members = append(members, recs[r].seq.Id())
+	}
+	if got := strings.Join(members, " "); got != "f a c" {
+		t.Errorf("group of f: %s, want f a c", got)
+	}
+}
+
+// TestAmbiguousSequences checks that a sequence with IUPAC letters is attached
+// to a cluster when it matches a center, and is left without cluster otherwise.
+func TestAmbiguousSequences(t *testing.T) {
+	root := "acgtacgtaccgtagctagcatcgatcgatcgtagctagctagcatcg"
+	db := obiseq.BioSequenceSlice{
+		makeSeq("center", root, 10, 0),
+		makeSeq("amb", root[:20]+"n"+root[21:], 5, 0), // matches the center
+		makeSeq("far", "ttttgggggccccaaaaattttgggggccccaaaaattttggggg", 4, 0),
+		makeSeq("ambfar", "nnnnttttggggcccccaaaa", 3, 0), // matches nothing, cannot be a center
+	}
+	p := Params{Threshold: 0.9, Ratio: 1, Normalized: true, SortKey: "count", AcceptAmbiguous: true, Workers: 2}
+	res := Cluster(db, p, nil)
+	out := res.Annotate()
+	got := map[string]string{}
+	for _, s := range out {
+		c, ok := s.GetStringAttribute("cluster")
+		if !ok {
+			c = "-"
+		}
+		got[s.Id()] = c
+	}
+	want := map[string]string{"center": "center", "amb": "center", "far": "far", "ambfar": "-"}
+	for id, w := range want {
+		if got[id] != w {
+			t.Errorf("%s: cluster %q, want %q", id, got[id], w)
+		}
+	}
+	if res.Clusters() != 2 {
+		t.Errorf("%d clusters, want 2", res.Clusters())
+	}
+	for _, s := range out {
+		if s.Id() == "ambfar" {
+			if center, _ := s.GetBoolAttribute("cluster_center"); center || s.HasAttribute("cluster_weight") {
+				t.Error("ambfar must have cluster_center=false and no weight")
+			}
+		}
+	}
+}
+
+// TestLengthTable checks that the values precomputed by length give the
+// scores of the direct computation, in every mode.
+func TestLengthTable(t *testing.T) {
+	rng := rand.New(rand.NewSource(33))
+	entries := randomEntries(rng, 120)
+	for i := 0; i < 20; i++ { // some very short sequences, which skip the filter
+		s := entries[i].seq[:8+rng.Intn(10)]
+		entries[i] = entry{seq: s, length: len(s), count: 1, table: buildTable4(s)}
+	}
+	lmax := 0
+	for i := range entries {
+		lmax = max(lmax, entries[i].length)
+	}
+	var buf obialign.BandedLCSBuffer
+	for _, ref := range []reference{refAlignment, refLongest, refShortest} {
+		for _, mode := range []scoring{
+			{threshold: 0.9, normalize: true, lcsmode: true},
+			{threshold: 0.8, normalize: true, lcsmode: false},
+			{threshold: 30, normalize: false, lcsmode: true},
+			{threshold: 6, normalize: false, lcsmode: false},
+		} {
+			direct := mode
+			direct.ref, direct.ratio = ref, 3
+			table := direct
+			table.prepareLengths(lmax)
+			if (ref == refShortest) != (table.byLength == nil) {
+				t.Fatalf("ref %v: table presence is wrong", ref)
+			}
+			for i := range entries {
+				for j := range entries {
+					a, b := direct.pairScore(&entries[i], &entries[j], -1, &buf), table.pairScore(&entries[i], &entries[j], -1, &buf)
+					if a != b {
+						t.Fatalf("ref %v mode %+v pair %d,%d: %v with the table, %v directly", ref, mode, i, j, b, a)
+					}
+				}
+			}
+		}
+	}
+}
+
+// TestBlockCommon checks the sums of a block of transposed tables against
+// commonWords.
+func TestBlockCommon(t *testing.T) {
+	width := simdBlockWidth()
+	if width == 0 {
+		t.Skip("blocks of tables are used with GOEXPERIMENT=simd only")
+	}
+	rng := rand.New(rand.NewSource(8))
+	seq := func(n int, alpha string) []byte {
+		s := make([]byte, n)
+		for i := range s {
+			s[i] = alpha[rng.Intn(len(alpha))]
+		}
+		return s
+	}
+	for it := 0; it < 200; it++ {
+		alpha := []string{"acgt", "ac", "a"}[it%3]
+		block := newTableBlock(width)
+		tabs := make([]*table4, width)
+		for j := range tabs {
+			tabs[j] = buildTable4(seq(rng.Intn(600), alpha))
+			block.set(width, j, tabs[j])
+		}
+		q := buildTable4(seq(rng.Intn(260), alpha))
+		words := sparseWords(q)
+		if words == nil {
+			continue
+		}
+		out := make([]uint8, 64)
+		block.common(width, words, out)
+		for j, tab := range tabs {
+			want := commonWordsRef(q, tab) - min(q.overflow, tab.overflow)
+			if int(out[j]) != want {
+				t.Fatalf("lane %d: %d, want %d", j, out[j], want)
+			}
+		}
+	}
+}

pkg/obitools/obiclust/options.go

@@ -3,102 +3,107 @@ package obiclust
 import (
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
 	"github.com/DavidGamba/go-getoptions"
+	log "github.com/sirupsen/logrus"
 )
 
-type ScoreNormalizationMode int
+// reference is the length used to normalize a score (or to express a raw
+// distance): the alignment length, the longest or the shortest sequence.
+type reference int
 
 const (
-	NoNormalization ScoreNormalizationMode = iota
-	NormalizedByShortest
-	NormalizedByLongest
-	NormalizedByAlignment
+	refAlignment reference = iota
+	refLongest
+	refShortest
 )
 
-var _sampleAttribute = "sample"
-var _threshold = 3.0
-var _shortReference = false
-var _longReference = false
-var _alignReference = true
-var _normalizedScore = false
-var _distanceMode = false
-var _exactMode = false
-var _ratioMax = 1.0
-var _sorted_by_length = false
-var _sorted_by_abundance = true
-var _sortingAscending = false
-var _onlyHead = false
-var _saveGraph = "__@@NOSAVE@@__"
-var _saveRatio = "__@@NOSAVE@@__"
-var _minSample = 1
+var _threshold = 0.97
+var _ratio = 1.0
+var _exact = false
+var _distance = false
+var _raw = false
+var _normalized = false
+var _refShortest = false
+var _refLongest = false
+var _refAlignment = false
+var _sortKey = "count"
+var _ascending = false
+var _acceptAmbiguous = false
+var _otuMap = ""
+var _noSequenceOutput = false
 
 func ObiclustOptionSet(options *getoptions.GetOpt) {
-	options.StringVar(&_sampleAttribute, "sample", _sampleAttribute,
-		options.Alias("s"),
-		options.Description("Attribute containing sample descriptions (default %s)."))
-
-	options.Float64Var(&_threshold, "distance", _threshold,
-		options.Alias("--threshold"),
-		options.Description("Threshold to merge sequences into the same cluster (default: %d)."))
-
-	options.Float64Var(&_ratioMax, "ratio", _ratioMax,
-		options.Alias("r"),
-		options.Description("Threshold ratio between counts (rare/abundant counts)"+
-			" of two sequence records so that the less abundant one is a variant of "+
-			"the more abundant (default: %3.2f)."))
-
-	options.BoolVar(&_onlyHead, "head", _onlyHead,
-		options.Alias("H"),
-		options.Description("Select only sequences with the head status in at least one sample."),
+	options.Float64Var(&_threshold, "threshold", _threshold,
+		options.Alias("t"),
+		options.ArgName("THRESHOLD"),
+		options.Description("Score threshold for clustering. If the score is normalized and expressed in similarity (default), "+
+			"it is an identity, e.g. 0.95 for an identity of 95%. If the score is normalized and expressed in distance, "+
+			"it is (1.0 - identity), e.g. 0.05 for an identity of 95%. If the score is not normalized and expressed in similarity, "+
+			"it is the length of the Longest Common Subsequence. If the score is not normalized and expressed in distance, "+
+			"it is (reference length - LCS length)."),
 	)
 
-	options.StringVar(&_saveGraph, "save-graph", _saveGraph,
-		options.Description("Creates a directory containing the set of DAG used by the obiclean clustering algorithm. "+
-			"The graph files follow the graphml format."),
-	)
+	options.BoolVar(&_refShortest, "shortest", _refShortest,
+		options.Alias("l"),
+		options.Description("Reference sequence length is the shortest."))
 
-	options.StringVar(&_saveRatio, "save-ratio", _saveRatio,
-		options.Description("Creates a file containing the set of abundance ratio on the graph edge. "+
-			"The ratio file follows the csv format."),
-	)
+	options.BoolVar(&_refLongest, "longest", _refLongest,
+		options.Alias("L"),
+		options.Description("Reference sequence length is the longest."))
 
-	options.IntVar(&_minSample, "min-sample-count", _minSample,
-		options.Description("Minimum number of samples a sequence must be present in to be considered in the analysis."),
-	)
+	options.BoolVar(&_refAlignment, "alignment", _refAlignment,
+		options.Alias("a"),
+		options.Description("Reference sequence length is the alignment length (default)."))
 
-	options.BoolVar(&_normalizedScore, "normalized-score", _normalizedScore,
+	options.BoolVar(&_normalized, "normalized", _normalized,
 		options.Alias("n"),
-		options.Description("Use alignment score normalized by length"),
-	)
+		options.Description("Score is normalized by the reference sequence length (default)."))
 
-	options.BoolVar(&_shortReference, "shortest", _shortReference,
-		options.Description("Use length of the shortest sequence to normalize alignment score."),
-	)
+	options.BoolVar(&_raw, "raw", _raw,
+		options.Alias("r"),
+		options.Description("Raw score, not normalized."))
 
-	options.BoolVar(&_longReference, "longest", _longReference,
-		options.Description("Use length of the longest sequence to normalize alignment score."),
-	)
+	options.BoolVar(&_distance, "distance", _distance,
+		options.Alias("d"),
+		options.Description("Score is expressed in distance (default: score is expressed in similarity)."))
 
-	options.BoolVar(&_alignReference, "alignment", _alignReference,
-		options.Description("Use alignment length to normalize alignment score."),
-	)
+	options.BoolVar(&_exact, "exact", _exact,
+		options.Alias("e"),
+		options.Description("A sequence is assigned to the cluster whose center presents the highest score "+
+			"above the threshold, as opposed to the default 'fast' mode where it is assigned to the first "+
+			"cluster found whose center presents a score above the threshold."))
 
-	options.BoolVar(&_distanceMode, "distance", _distanceMode,
-		options.Description("Use alignment distance instead of similarity score."),
-	)
+	options.Float64Var(&_ratio, "ratio", _ratio,
+		options.Alias("R"),
+		options.ArgName("RATIO"),
+		options.Description("Maximum ratio between the counts of two sequences so that the less abundant one "+
+			"can be considered as a variant of the more abundant one (default: %3.2f)."))
 
-	options.BoolVar(&_exactMode, "exact", _exactMode,
-		options.Description("Use exact clustering algorithm (default is greedy)."),
-	)
+	options.StringVar(&_sortKey, "sort", _sortKey,
+		options.Alias("s"),
+		options.ArgName("KEY"),
+		options.Description("Sort the sequences on KEY before clustering. KEY must be 'None' for no sorting, "+
+			"or an attribute of the sequences, except for the count that can be computed (default: sorting on count). "+
+			"The sequences are sorted in decreasing order (see --ascending), ties being ordered "+
+			"as in the input."))
 
-	options.BoolVar(&_sorted_by_length, "length-ordered", _sorted_by_length,
-		options.Description("Sort sequence by length before clustering."),
-	)
-	options.BoolVar(&_sorted_by_abundance, "abundance-ordered", _sorted_by_abundance,
-		options.Description("Sort sequence by read counts (abundance) before clustering."),
-	)
-	options.BoolVar(&_sortingAscending, "ascending-sorting", _sortingAscending,
-		options.Description("Sort order is ascending (default is descending)."),
-	)
+	options.BoolVar(&_ascending, "ascending", _ascending,
+		options.Description("Sorting is in ascending order (default: descending)."))
+
+	options.BoolVar(&_acceptAmbiguous, "accept-ambiguous", _acceptAmbiguous,
+		options.Alias("g"),
+		options.Description("Accept the sequences containing IUPAC letters other than a, c, g and t. "+
+			"Such a sequence can be attached to a cluster (the alignment handles the IUPAC codes), "+
+			"but cannot be the center of a cluster, and is left without cluster if it matches no center "+
+			"(default: these sequences are discarded)."))
+
+	options.StringVar(&_otuMap, "otu-map", _otuMap,
+		options.ArgName("FILENAME"),
+		options.Description("Write the clusters to FILENAME as a CSV table, one row per sequence "+
+			"(id, cluster, cluster_center, cluster_score, count), grouped by cluster."))
+
+	options.BoolVar(&_noSequenceOutput, "no-sequence-output", _noSequenceOutput,
+		options.Alias("f"),
+		options.Description("Do not write the sequences on the standard output."))
 }
 
 func OptionSet(options *getoptions.GetOpt) {
@@ -107,44 +112,63 @@ func OptionSet(options *getoptions.GetOpt) {
 	ObiclustOptionSet(options)
 }
 
-// It returns the name of the attibute used to store sample name
-func CLISampleAttribute() string {
-	return _sampleAttribute
-}
+// CLIThreshold returns the clustering threshold as given on the command line.
+func CLIThreshold() float64 { return _threshold }
 
-func CLIThreshold() float64 {
-	return _threshold
-}
+// CLIRatio returns the maximum abundance ratio between a sequence and the center it is attached to.
+func CLIRatio() float64 { return _ratio }
 
-// Returns true it the obliclean graphs must be saved
-func CLISaveGraphToFiles() bool {
-	return _saveGraph != "__@@NOSAVE@@__"
-}
+// CLIExact returns true when a sequence must be attached to the best center and not to the first matching one.
+func CLIExact() bool { return _exact }
 
-// It returns the directory where the graph files are saved
-func CLIGraphFilesDirectory() string {
-	return _saveGraph
-}
+// CLIDistance returns true when the score is expressed in distance.
+func CLIDistance() bool { return _distance }
 
-// Returns true it the table of ratio must be saved
-func CLIIsSaveRatioTable() bool {
-	return _saveRatio != "__@@NOSAVE@@__"
-}
-
-// It returns the filename of the file that stores the ratio table
-func CLIRatioTableFilename() string {
-	return _saveRatio
-}
-
-func CLINormalizationMode() ScoreNormalizationMode {
-	switch {
-	case _alignReference:
-		return NormalizedByAlignment
-	case _longReference:
-		return NormalizedByLongest
-	case _shortReference:
-		return NormalizedByShortest
-	default:
-		return NoNormalization
+// CLINormalized returns true when the score is normalized by the reference length.
+func CLINormalized() bool {
+	if _raw && _normalized {
+		log.Fatal("The options --raw and --normalized are exclusive")
 	}
+	return !_raw
 }
+
+// CLIReference returns the length used as reference to normalize the score.
+func CLIReference() reference {
+	n := 0
+	ref := refAlignment
+	if _refShortest {
+		n++
+		ref = refShortest
+	}
+	if _refLongest {
+		n++
+		ref = refLongest
+	}
+	if _refAlignment {
+		n++
+	}
+	if n > 1 {
+		log.Fatal("The options --shortest, --longest and --alignment are exclusive")
+	}
+	return ref
+}
+
+// CLISortKey returns the key used to sort the sequences, or "None".
+func CLISortKey() string {
+	if _sortKey == "none" {
+		return "None"
+	}
+	return _sortKey
+}
+
+// CLIAscending returns true when the sort must be in ascending order.
+func CLIAscending() bool { return _ascending }
+
+// CLIAcceptAmbiguous returns true when the sequences with IUPAC letters other than acgt are kept.
+func CLIAcceptAmbiguous() bool { return _acceptAmbiguous }
+
+// CLIOTUMap returns the name of the OTU map file, empty if none is requested.
+func CLIOTUMap() string { return _otuMap }
+
+// CLINoSequenceOutput returns true when the sequences must not be written.
+func CLINoSequenceOutput() bool { return _noSequenceOutput }

pkg/obitools/obiclust/output.go

@@ -0,0 +1,128 @@
+package obiclust
+
+import (
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiitercsv"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
+)
+
+// Annotate writes the result of the clustering on the sequences and returns
+// them in the order sumaclust writes them: the groups of identical sequences
+// in their sorted order, each group beginning with its head.
+//
+// Every sequence receives
+//   - cluster: the identifier of the center of its cluster;
+//   - cluster_score: the score with this center;
+//   - cluster_center: true for the center only;
+//   - cluster_weight: the cumulated count of the sequences of the cluster.
+//
+// A sequence with IUPAC letters that matches no center belongs to no cluster:
+// it only gets cluster_center=false.
+func (res *Result) Annotate() obiseq.BioSequenceSlice {
+	recs, groups, cl := res.recs, res.groups, res.clustered
+	weight := make([]int, len(groups))
+	for g := range groups {
+		if cl.center[g] >= 0 {
+			weight[cl.center[g]] += groups[g].count
+		}
+	}
+
+	out := make(obiseq.BioSequenceSlice, 0, len(recs))
+	for g, grp := range groups {
+		ctr := cl.center[g]
+
+		for r := grp.start; r < grp.end; r++ {
+			s := recs[r].seq
+			if ctr < 0 {
+				// a sequence with IUPAC letters that matches no center
+				s.RemoveAttribute("cluster")
+				s.RemoveAttribute("cluster_score")
+				s.RemoveAttribute("cluster_weight")
+				s.SetAttribute("cluster_center", false)
+				out = append(out, s)
+				continue
+			}
+			centerID := recs[groups[ctr].start].seq.Id()
+			s.SetAttribute("cluster", centerID)
+			s.SetAttribute("cluster_score", cl.score[g])
+			s.SetAttribute("cluster_center", ctr == g && r == grp.start)
+			s.SetAttribute("cluster_weight", weight[ctr])
+			out = append(out, s)
+		}
+	}
+	return out
+}
+
+// OTUMapIterator describes the clusters as a CSV table, one row per sequence:
+//   - id: the identifier of the sequence;
+//   - cluster: the identifier of the center of its cluster;
+//   - cluster_center: true for the center only;
+//   - cluster_score: the score with this center;
+//   - count: the count of the sequence.
+//
+// The rows are grouped by cluster, in the order the clusters were created. In
+// a cluster, the center comes first, followed by the sequences identical to
+// it, then by the other members, each followed by its identical sequences.
+// The sequences without cluster (see Annotate) come last, with no cluster nor
+// score.
+func (res *Result) OTUMapIterator(source string, batchSize int) *obiitercsv.ICSVRecord {
+	recs, groups, cl := res.recs, res.groups, res.clustered
+
+	iterator := obiitercsv.NewICSVRecord()
+	iterator.Add(1)
+	for _, field := range []string{"id", "cluster", "cluster_center", "cluster_score", "count"} {
+		iterator.AppendField(field)
+	}
+
+	members := make(map[int][]int, len(cl.centers))
+	var orphans []int
+	for g := range groups {
+		if ctr := cl.center[g]; ctr >= 0 {
+			members[ctr] = append(members[ctr], g)
+		} else {
+			orphans = append(orphans, g)
+		}
+	}
+
+	go func() {
+		iterator.WaitAndClose()
+	}()
+
+	go func() {
+		order := 0
+		batch := make([]obiitercsv.CSVRecord, 0, batchSize)
+		add := func(g int) {
+			ctr := cl.center[g]
+			for r := groups[g].start; r < groups[g].end; r++ {
+				row := obiitercsv.CSVRecord{
+					"id":             recs[r].seq.Id(),
+					"cluster_center": ctr == g && r == groups[g].start,
+					"count":          recs[r].count,
+				}
+				if ctr >= 0 {
+					row["cluster"] = recs[groups[ctr].start].seq.Id()
+					row["cluster_score"] = cl.score[g]
+				}
+				batch = append(batch, row)
+				if len(batch) == batchSize {
+					iterator.Push(obiitercsv.MakeCSVRecordBatch(source, order, batch))
+					order++
+					batch = make([]obiitercsv.CSVRecord, 0, batchSize)
+				}
+			}
+		}
+		for _, ctr := range cl.centers {
+			for _, g := range members[ctr] {
+				add(g)
+			}
+		}
+		for _, g := range orphans {
+			add(g)
+		}
+		if len(batch) > 0 || order == 0 {
+			iterator.Push(obiitercsv.MakeCSVRecordBatch(source, order, batch))
+		}
+		iterator.Done()
+	}()
+
+	return iterator
+}

pkg/obitools/obiclust/prepare.go

@@ -0,0 +1,178 @@
+package obiclust
+
+import (
+	"bytes"
+	"sort"
+	"strconv"
+	"strings"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
+	log "github.com/sirupsen/logrus"
+)
+
+// record is a sequence of the dataset.
+type record struct {
+	seq       *obiseq.BioSequence
+	pos       int    // position in the dataset
+	clean     []byte // the nucleotides of the sequence, in lower case
+	count     int
+	key       float64 // value of the sorting key
+	ambiguous bool    // contains IUPAC letters other than a, c, g and t
+}
+
+// group is a run of identical sequences: recs[start] is its head, the
+// following ones are the duplicates. count is the cumulated count, key the
+// value of the sorting key of the head.
+type group struct {
+	start, end int
+	count      int
+	key        float64
+}
+
+// nucleotide classes of a byte
+const (
+	notNucleotide = iota
+	plainNucleotide
+	ambiguousNucleotide
+)
+
+var nucleotideClass = func() (t [256]uint8) {
+	for _, c := range "acgt" {
+		t[c] = plainNucleotide
+	}
+	for _, c := range "umrwsykvhdbn" {
+		t[c] = ambiguousNucleotide
+	}
+	return t
+}()
+
+// classify returns the nucleotides of a sequence and tells if it contains
+// IUPAC letters other than a, c, g and t. nil is returned if the sequence is
+// empty, or contains anything else than IUPAC letters (and also IUPAC letters
+// other than a, c, g and t unless ambiguous ones are accepted).
+func classify(s []byte, acceptAmbiguous bool) (clean []byte, ambiguous bool) {
+	if len(s) == 0 {
+		return nil, false
+	}
+	for _, c := range s {
+		switch nucleotideClass[c] {
+		case notNucleotide:
+			return nil, false
+		case ambiguousNucleotide:
+			if !acceptAmbiguous {
+				return nil, false
+			}
+			ambiguous = true
+		}
+	}
+	return s, ambiguous
+}
+
+// atof reads the leading number of a string as C atof does.
+func atof(v interface{}) float64 {
+	if s, ok := v.(string); ok {
+		s = strings.TrimSpace(s)
+		for n := len(s); n > 0; n-- {
+			if f, err := strconv.ParseFloat(s[:n], 64); err == nil {
+				return f
+			}
+		}
+		return 0
+	}
+	f, err := obiutils.InterfaceToFloat64(v)
+	if err != nil {
+		return 0
+	}
+	return f
+}
+
+// sortKeyOf returns the value of the sorting key of a sequence.
+func sortKeyOf(s *obiseq.BioSequence, key string) float64 {
+	if key == "count" {
+		return float64(s.Count())
+	}
+	v, ok := s.GetAttribute(key)
+	if !ok {
+		log.Fatalf("'%s' is not an attribute of the sequence %s", key, s.Id())
+	}
+	return atof(v)
+}
+
+// prepare reads the sequences, groups the identical ones and orders them.
+//
+// The order is fully determined, whatever the sorting algorithm:
+//
+//  1. the records of a group of identical sequences are ordered on the
+//     sorting key (decreasing, increasing if ascending), then on their
+//     position in the dataset; the first one is the head of the group, whose
+//     identifier names the cluster if it is a center;
+//  2. the groups are ordered on the sorting key of their head (the count of
+//     the whole group if the key is "count"), then on the position of the
+//     head in the dataset. With the key "None" they are in the order of the
+//     first occurrence of their sequence.
+//
+// The sequences containing anything else than a, c, g and t are discarded,
+// except if acceptAmbiguous is set and they only contain IUPAC letters: they
+// are then kept, but cannot be the center of a cluster.
+func prepare(db obiseq.BioSequenceSlice, key string, ascending, acceptAmbiguous bool) ([]record, []group, int) {
+	recs := make([]record, 0, len(db))
+	discarded := 0
+
+	for pos, s := range db {
+		clean, ambiguous := classify(s.Sequence(), acceptAmbiguous)
+		if clean == nil {
+			discarded++
+			continue
+		}
+		r := record{seq: s, pos: pos, clean: clean, count: s.Count(), ambiguous: ambiguous}
+		if key != "None" {
+			r.key = sortKeyOf(s, key)
+		}
+		recs = append(recs, r)
+	}
+
+	// before reports whether a is ranked before b by the sorting key
+	before := func(a, b float64) bool {
+		if ascending {
+			return a < b
+		}
+		return a > b
+	}
+
+	sort.Slice(recs, func(i, j int) bool {
+		a, b := &recs[i], &recs[j]
+		if c := bytes.Compare(a.clean, b.clean); c != 0 {
+			return c < 0
+		}
+		if a.key != b.key && key != "None" {
+			return before(a.key, b.key)
+		}
+		return a.pos < b.pos
+	})
+
+	groups := make([]group, 0, len(recs))
+	for i := 0; i < len(recs); {
+		j, count := i+1, recs[i].count
+		for j < len(recs) && bytes.Equal(recs[j].clean, recs[i].clean) {
+			count += recs[j].count
+			j++
+		}
+		g := group{start: i, end: j, count: count, key: recs[i].key}
+		if key == "count" {
+			g.key = float64(count)
+		}
+		groups = append(groups, g)
+		i = j
+	}
+
+	sort.Slice(groups, func(i, j int) bool {
+		a, b := &groups[i], &groups[j]
+		if key != "None" && a.key != b.key {
+			return before(a.key, b.key)
+		}
+		return recs[a.start].pos < recs[b.start].pos
+	})
+
+	return recs, groups, discarded
+}

pkg/obitools/obiclust/score.go

@@ -0,0 +1,233 @@
+package obiclust
+
+import (
+	"math"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obialign"
+	log "github.com/sirupsen/logrus"
+)
+
+// entry is a distinct sequence of the dataset with what the clustering needs.
+type entry struct {
+	seq    []byte
+	length int
+	count  int // cumulated count of the identical sequences
+	table  *table4
+	sparse []uint16 // words of the table (see sparseWords), nil if unusable
+	// ambiguous sequences contain IUPAC letters other than a, c, g and t:
+	// they have no 4-mer table, and cannot be the center of a cluster
+	ambiguous bool
+}
+
+// scoring holds the way sumaclust scores a pair of sequences and decides
+// whether it passes the threshold. It reproduces the arithmetic of the
+// reference implementation (integer truncations, floating point
+// comparisons) so that the same pairs are accepted with the same scores.
+type scoring struct {
+	threshold float64 // threshold as used for the comparison (1 - t for a normalized distance)
+	normalize bool
+	lcsmode   bool // true: score is a similarity, false: it is a distance
+	ref       reference
+	ratio     float64
+	worst     float64 // score of a pair that cannot be attached
+
+	// byLength gives, for the pairs whose longest sequence has a length l,
+	// the values that depend on l only. It is built when the reference is not
+	// the shortest sequence, otherwise those values depend on both lengths.
+	byLength []lengthInfo
+}
+
+type lengthInfo struct {
+	lcsMin    int32 // see lcsMin
+	minCommon int32 // see minCommon
+}
+
+// prepareLengths fills byLength for the lengths up to lmax.
+func (sc *scoring) prepareLengths(lmax int) {
+	if sc.ref == refShortest {
+		return
+	}
+	sc.byLength = make([]lengthInfo, lmax+1)
+	for l := range sc.byLength {
+		sc.byLength[l] = lengthInfo{int32(sc.lcsMin(l, l)), int32(sc.minCommon(l, l))}
+	}
+}
+
+// similarityLike tells if the comparison with the threshold is "score >= threshold".
+func (sc *scoring) similarityLike() bool { return sc.lcsmode || sc.normalize }
+
+// lcsMin is the smallest LCS score that a pair of lengths l1 >= l2 can have
+// and still pass the threshold (calculateLCSmin of sumaclust).
+func (sc *scoring) lcsMin(l1, l2 int) int {
+	switch {
+	case sc.threshold <= 0:
+		return 0
+	case sc.normalize:
+		if sc.ref == refShortest {
+			return int(sc.threshold * float64(l2))
+		}
+		return int(sc.threshold * float64(l1))
+	case sc.lcsmode:
+		return int(sc.threshold)
+	case sc.ref == refShortest:
+		return int(float64(l2) - sc.threshold)
+	default:
+		return int(float64(l1) - sc.threshold)
+	}
+}
+
+// minCommon is the number of 4-mers that two sequences of lengths l1 >= l2
+// must share to be possibly similar enough (isPossibleSumathings).
+func (sc *scoring) minCommon(l1, l2 int) int {
+	reflen := l2
+	if sc.ref == refAlignment || sc.ref == refLongest {
+		reflen = l1
+	}
+	var lcs int
+	if sc.normalize {
+		lcs = int(math.Ceil(float64(reflen) * sc.threshold))
+	} else {
+		th := sc.threshold
+		if !sc.lcsmode {
+			th = float64(reflen) - th
+		}
+		lcs = int(th)
+	}
+	return minCommonWords(l1, lcs)
+}
+
+// pairScore returns the score of a query sequence against a center, or the
+// worst score when the pair cannot be attached.
+//
+// common, if not negative, is the sum of the minima of the 4-mer counters of
+// the two sequences, already computed by a block of tables.
+func (sc *scoring) pairScore(q, c *entry, common int, buf *obialign.BandedLCSBuffer) float64 {
+	// The quotient of two counts is not above 1 when the first is not above
+	// the second, which spares the division in the usual case.
+	if !(sc.ratio >= 1 && q.count <= c.count) && float64(q.count)/float64(c.count) > sc.ratio {
+		return sc.worst
+	}
+
+	l1, l2 := q.length, c.length
+	long, short := q, c
+	if l1 < l2 {
+		l1, l2 = l2, l1
+		long, short = c, q
+	}
+	var lcsMin, minCommon int
+	if sc.byLength != nil {
+		info := sc.byLength[l1]
+		lcsMin, minCommon = int(info.lcsMin), int(info.minCommon)
+	} else {
+		lcsMin, minCommon = sc.lcsMin(l1, l2), sc.minCommon(l1, l2)
+	}
+	if l2 < lcsMin {
+		return sc.worst
+	}
+	// The 4-mer filter counts identical words: it does not hold when IUPAC
+	// codes can match different letters. It lets short sequences pass.
+	if l1 >= 12 && l2 >= 12 && !long.ambiguous && !short.ambiguous {
+		if common >= 0 {
+			common += min(long.table.overflow, short.table.overflow)
+		} else {
+			common = commonWords(long.table, short.table)
+		}
+		if common < minCommon {
+			return sc.worst
+		}
+	}
+
+	// The length of the alignment is needed only to normalize by it, or to
+	// express a distance with it; the score alone is much cheaper.
+	var lcs, alilen int
+	var err error
+	if sc.ref == refAlignment && (sc.normalize || !sc.lcsmode) {
+		lcs, alilen, err = buf.AtLeast(q.seq, c.seq, lcsMin)
+	} else {
+		lcs, err = buf.ScoreAtLeast(q.seq, c.seq, lcsMin)
+	}
+	if err != nil {
+		log.Fatalf("Cannot align two sequences: %v", err)
+	}
+	if lcs < 0 {
+		// The best alignment has a score under lcsMin: the pair cannot pass.
+		return sc.worst
+	}
+
+	id := float64(lcs)
+	if !sc.lcsmode && !sc.normalize {
+		switch sc.ref {
+		case refAlignment:
+			id = float64(alilen) - id
+		case refLongest:
+			id = float64(l1) - id
+		case refShortest:
+			id = float64(l2) - id
+		}
+	}
+	if sc.normalize {
+		switch sc.ref {
+		case refAlignment:
+			id /= float64(alilen)
+		case refLongest:
+			id /= float64(l1)
+		case refShortest:
+			id /= float64(l2)
+		}
+	}
+	return id
+}
+
+// beats tells if the score s is better than the score best (without any
+// threshold).
+func (sc *scoring) beats(s, best float64) bool {
+	if sc.similarityLike() {
+		return s > best
+	}
+	return s < best
+}
+
+// lcsMinFor is lcsMin for sequences of lengths l1 >= l2, from the table when it exists.
+func (sc *scoring) lcsMinFor(l1, l2 int) int {
+	if sc.byLength != nil {
+		return int(sc.byLength[l1].lcsMin)
+	}
+	return sc.lcsMin(l1, l2)
+}
+
+// lengthCompatible tells if two sequences of these lengths may be similar enough:
+// the shortest cannot be shorter than the minimum LCS score of the pair.
+func (sc *scoring) lengthCompatible(la, lb int) bool {
+	l1, l2 := max(la, lb), min(la, lb)
+	return l2 >= sc.lcsMinFor(l1, l2)
+}
+
+// selects tells if a pair of score s must replace the best pair found so far,
+// of score best.
+func (sc *scoring) selects(s, best float64) bool {
+	if sc.similarityLike() {
+		return s >= sc.threshold && s > best
+	}
+	return s <= sc.threshold && s < best
+}
+
+// centerScore is the score of a sequence with itself.
+func (sc *scoring) centerScore(length int) float64 {
+	switch {
+	case sc.normalize && sc.lcsmode:
+		return 1.0
+	case !sc.lcsmode:
+		return 0.0
+	default:
+		return float64(length)
+	}
+}
+
+// memberScore is the score reported for a sequence attached to a center
+// with the score s.
+func (sc *scoring) memberScore(s float64) float64 {
+	if !sc.lcsmode && sc.normalize {
+		return 1.0 - s
+	}
+	return s
+}

pkg/obitools/obiclust/testdata/cases.txt

@@ -0,0 +1,9 @@
+families	default	-t 0.9
+families	exact	-t 0.9 -e
+families	shortest	-t 0.9 -l -e
+families	longest	-t 0.85 -L
+families	distance	-t 0.1 -d
+families	rawdist	-t 4 -r -d -e
+families	rawlcs	-t 40 -r
+families	ratio	-t 0.9 -R 0.5
+families	ascending	-t 0.9 -o

pkg/obitools/obiclust/testdata/families_ascending.expected

@@ -0,0 +1,101 @@
+f5v2s55	f5v2s55	1.000000	T	666	cggcatcgcaccataagatggtaatcactaaaaaaatcggcctaacctgtccatatcgccact
+f1v6s15	f1v6s15	1.000000	T	3070	gaatcagcttctaaccaagcgttgcagaaccggctactttaagcatgatgaatgcgtcgtaagtgatactcgacgattc
+f7v2s66	f7v2s66	1.000000	T	3988	gcttcgtgggaaccagaacaaccgacatattccgaaccaccggacatacgatccttaaacc
+f4v7s51	f4v7s51	1.000000	T	8599	cgtttattcgtaggatctactacgcatcaaagtatcccacttttgtaccccactaagagcaga
+f5v1s54	f5v1s54	1.000000	T	9091	cggaacgcaccataagatggtaatcactaaaaaaatcggcctaacctgtccatatcgccactt
+f7v1s65	f7v1s65	1.000000	T	11279	gcttcggggaaccagagacaaccgacatatttcgaaccaccgacatacgatcctttaaacc
+f3v8s39	f3v8s39	1.000000	T	13623	cgaaaaaggtgaatgaaaggcctgggacgctcctggttggggcgctctaggtgtgtggcttgaacgttagacct
+f4v4s48	f4v4s48	1.000000	T	15906	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagagaaa
+f3v11s42	f3v11s42	1.000000	T	18309	cgaaaaaggtgaatgaaagtctgggacgctcctggtttgggacgctctaggtgttgtggcttgaacgttagcacct
+f6v3s63	f6v3s63	1.000000	T	19024	catgtcaagagactggaaccccggtgatgtgaaaaaaggttttgggtcacgtctccatggctacg
+f11v3s94	f11v3s94	1.000000	T	21189	agcgttagcaaagagcctggttaatcgccgtcgaaggatcggtggtgatcagagatgcgggcatccgtttc
+f2v6s24	f2v6s24	1.000000	T	21984	tggactagtagacgtgtgcctcatcgacgcgtgagacactttgatttcttatacggcgtctcag
+f0v8s8	f0v8s8	1.000000	T	24872	ggatcacagtcctacactgctcactccaaccccggccctgagtccgaggagagggtgcttcagagtatgtataccactg
+f7v3s67	f7v3s67	1.000000	T	26251	gcttcgtgggaccagagacaaccgacatatttcgaaccaccgacatacgatccttaaacc
+f2v9s27	f2v9s27	1.000000	T	26719	tggactagtagaccgtgtgcctaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f4v5s49	f4v5s49	1.000000	T	26933	ctatattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagagaagca
+f11v9s100	f11v9s100	1.000000	T	27405	agcgttagcaaaggagcctggttaatcgccctcgaggatcggtggtgatcagagatgcgggcatccgtttc
+f2v12s30	f2v12s30	1.000000	T	27908	tggactagtagaccgtgtgccacaatcgacgctgaggacacgttgatttttatacggcgtctcag
+f9v0s76	f9v0s76	1.000000	T	29993	gggatcgtggcaagcaacccttgccgcctcgactgcggctaaagacgcatgttccagtaataccta
+f4v6s50	f4v6s50	1.000000	T	30723	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagacgaagag
+f6v2s62	f6v2s62	1.000000	T	33001	catgtcgagagactggaaccccggtgatgtgaaaaaaggtcttgggtacgtcccatggctac
+f11v5s96	f11v5s96	1.000000	T	33026	agcgttagcaaagagcctggttaatggccctcgaggatcggtggctgaccagagatgcgggcatccgtttc
+f8v1s69	f8v1s69	1.000000	T	33813	aagaccttgaacacctctaagcgaaaattggatatcgagtcagggaacataaccacgggtgcgt
+f11v4s95	f11v4s95	1.000000	T	34530	agcgttagcaaagagcctggttaatcccctcgagatcgggtggtgatcagagatgcgggcatccgtttc
+f3v9s40	f3v9s40	1.000000	T	35203	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggggttgtggcttgaacgttagcacct
+f11v2s93	f11v2s93	1.000000	T	35758	agcgttagcaaagagcctggttaatcgccctcggaggatcggtggtgatcagagatgcgggcatccgttc
+f10v6s83	f10v6s83	1.000000	T	36011	ttccggacactcgcaatcttccaagcagaggtccagctaacacacagcaggcatttagtcctgatgggtagc
+f3v7s38	f3v7s38	1.000000	T	36703	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttcgtgcttgaacgttagcacct
+f3v10s41	f3v10s41	1.000000	T	37492	cgaaaataaggtgaatgaaagggtgggacgctcctagtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f5v4s57	f5v4s57	1.000000	T	38613	cggcaacgcaccataagatggtaatcactaaaaaaatcggcctaacctgtccatatcgccactat
+f10v1s78	f10v1s78	1.000000	T	43528	ttgccggacactcgcaatcctccaagcagaggtccagctaacacacagcaggcatttagtcccgatgaggtagc
+f10v8s85	f10v8s85	1.000000	T	46704	ttgccggacactcgaatcttccaagcagaggtccagctaacacacagcaggcatactagtcccgatgggtagc
+f6v0s60	f6v0s60	1.000000	T	48958	catgtcaagagactggaaccccggtgatgtgaaaaaaggtcttgggtacgtcccatggctacg
+f8v6s74	f8v6s74	1.000000	T	49062	aagacccttgaacacctctaagcgaaaattggattcgagtcagggaacataaccacgggtgccgt
+f1v0s9	f1v0s9	1.000000	T	49791	gaatcagcttctaaccaagcgatgcagaaccggctactttaagcattgatgaatgcgtcgtaagtgatactcgacgattc
+f5v5s58	f5v5s58	1.000000	T	49852	cgcaacgcaccattaagatggtaatcactaaaaaaatcggcctaacctgtccaatcgccactt
+f0v5s5	f0v5s5	1.000000	T	54120	ggatcacagtctacactgctcactcccccccggcccctgagtccgaggagagggtgcttcaaagtatgtataccactg
+f4v1s45	f4v1s45	1.000000	T	55908	ctgtatttcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactatagagaaga
+f11v6s97	f11v6s97	1.000000	T	58908	agcgttagcaaagaacctggttaatcgccctcgaggatcggtggtggatcggagatgcgggcatcgcgtttc
+f3v4s35	f3v4s35	1.000000	T	59170	cgaaaaaggtgaagaaaggctgggacgctcctggttggcgcgctctaggtgttgtggcttgaacgttagcaccta
+f3v1s32	f3v1s32	1.000000	T	59632	cgaaaaagagtgaatgaaatggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f8v4s72	f8v4s72	1.000000	T	59724	aagacttgaacacctctaagcgaaaattggattcgagtcagggaacataaccacgggtgcgt
+f8v5s73	f8v5s73	1.000000	T	64084	aagaccttgtacacctctaagcgataaattggattcgagtcagggaacataaccacggatgcgt
+f11v0s91	f11v0s91	1.000000	T	66160	agcgttagcaaagagcctggttaatcgccctcgaggatcggtggtgatcagagatgcgggcatccgtttc
+f10v10s87	f10v10s87	1.000000	T	66794	tctgccggacactcgcaatcttccaagcagaggtccagctaacacacgcaggcatttatccgatgggtagc
+f4v3s47	f4v3s47	1.000000	T	69396	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaaagaaga
+f8v3s71	f8v3s71	1.000000	T	70497	aagaccttgaacacctctaagcgaaattggattcgagtcagcgaacataacacgggtgcgt
+f3v2s33	f3v2s33	1.000000	T	70860	cgaaaaaaggtaatgaaaggctgggatgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcact
+f11v1s92	f11v1s92	1.000000	T	71853	agcgttagcaaagagcctggttcatcgccctcgaggatcggtggtgatcaagagatgcggcatccgtttc
+f7v0s64	f7v0s64	1.000000	T	72498	gcttcgtgggaaccagagacaaccgacatatttcgaaccaccgacatacgatccttaaacc
+f11v8s99	f11v8s99	1.000000	T	72674	agcgttagcaaagagcctggttaatctgccctcgaggatcggtggtgatcagagatgcgggcatccgtttc
+f8v2s70	f8v2s70	1.000000	T	74088	aagaccttgaacaacctctaagccgaaattggaattcgagtcagggaacataaccacgggtgcgat
+f4v2s46	f4v2s46	1.000000	T	74433	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagagaaga
+f10v12s89	f10v12s89	1.000000	T	74438	ttgccggacactcgcaatcttccaagcagaggtccagctaacacacacgcaggcatttagacccgatgggtagc
+f8v7s75	f8v7s75	1.000000	T	75803	aagaccttgaacacctctaagcgaaaattggattccagtcagggaaccataaccacgggtgcgt
+f3v5s36	f3v5s36	1.000000	T	76948	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttatggcttgaaagttagcacct
+f10v11s88	f10v11s88	1.000000	T	78894	ttgccggacactcgcaatcttccaagcagaggtccagctaactcacagccaggcatttagtcccgatgggtagc
+f1v8s17	f1v8s17	1.000000	T	79492	gaatcaggttcttccaagcgctgcagaaccggctactttaagcattgatgaatgcgtcagtaagtgatacccgacgattc
+f2v1s19	f1v8s17	1.000000	F	79492	gaatcaggttcttccaagcgctgcagaaccggctactttaagcattgatgaatgcgtcagtaagtgatacccgacgattc
+f8v0s68	f8v0s68	1.000000	T	80207	aagaccttgaacacctctaagcgaaaattggattcgagtcagggaacataaccacgggtgcgt
+f3v12s43	f3v12s43	1.000000	T	80835	cgaaaaaggtgaatgaaagactgggacgcctcctggtttgggacgctctaggtggttgtggcttgaacgttagcacct
+f2v5s23	f2v5s23	1.000000	T	81657	gaatcagcttcaaccaagcgatgcagaaccgctgctttaagcatgatgaatcgtcgtaagtgatactcgacgattc
+f1v7s16	f2v5s23	1.000000	F	81657	gaatcagcttcaaccaagcgatgcagaaccgctgctttaagcatgatgaatcgtcgtaagtgatactcgacgattc
+f0v2s2	f0v2s2	1.000000	T	83299	ggatcacagtctacactgctcactccaaccccggcccctgagtccgaggagagggtgcttcagagtatgtataccactg
+f0v0s0	f0v2s2	1.000000	F	83299	ggatcacagtctacactgctcactccaaccccggcccctgagtccgaggagagggtgcttcagagtatgtataccactg
+f1v3s12	f1v3s12	1.000000	T	84418	ggatcacagtctacactgctccctccaaccccggcccctggtccgaggagagggtgcttcagagtattataccactg
+f0v6s6	f1v3s12	1.000000	F	84418	ggatcacagtctacactgctccctccaaccccggcccctggtccgaggagagggtgcttcagagtattataccactg
+f2v11s29	f2v11s29	1.000000	T	85592	tggactgtagaaccgtgtgcctcaatccacgcgtgaggacacgttgatttcttatacggcgtctcag
+f4v8s52	f4v8s52	1.000000	T	86639	ctgatattcgtattgatctactacgtatcaaagtatcccacttttgtgaccccactaagagaaga
+f10v5s82	f10v5s82	1.000000	T	87843	ttgccggacactcgcaatcttccaagcagaggtccagctaacacatagcaggcatttagtcccgatgggtagc
+f10v4s81	f10v4s81	1.000000	T	88973	ttgccggacactggcaatcttccatagcagaggtccagctaacacacagcaggcatttagtcccgatgggtagc
+f1v4s13	f1v4s13	1.000000	T	90139	gaatcagcttctcaaccaagcgatgcagaaccggctactttaagcattgatgaatgcgtcgtaagtgatactggacgattc
+f10v13s90	f10v13s90	1.000000	T	92493	tgccggacactcgcaatctccaagcagagagtccaagctaacacacagcaggcatttgtcccgatgggtagc
+f10v2s79	f10v2s79	1.000000	T	93964	ttgccggtcactcgcaatcttaccaaccagaggtccagctaacacacagcaggcatttagtcccgatgggtagc
+f5v3s56	f5v3s56	1.000000	T	94426	ccgcaacgcaccataagatgtaatcactaagaaaaatcggcctaacctgtcatatcgccactt
+f0v3s3	f0v3s3	1.000000	T	95466	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f0v1s1	f0v3s3	1.000000	F	95466	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f0v4s4	f0v3s3	1.000000	F	95466	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f1v5s14	f0v3s3	1.000000	F	95466	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f2v10s28	f2v10s28	1.000000	T	97350	ggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f5v6s59	f2v10s28	1.000000	F	97350	ggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f10v0s77	f10v0s77	1.000000	T	97674	ttgccggacactcgcaatcttccaagcagaggtccagctaacacacagcaggcatttagtcccgatgggtagc
+f10v7s84	f10v7s84	1.000000	T	98678	gtgccggacactcgcaatcttcacaagcagaggtccagctaacacacagcagcatttagtcccgatgggtagc
+f2v4s22	f2v4s22	1.000000	T	99661	tggactagtagaccgtgtcgcctcaatcgacgcgtgaggacacgttgattcttatacggcgtctcag
+f11v7s98	f11v7s98	1.000000	T	167833	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgtctctaggttgttgtggctgaacgtagcact
+f5v0s53	f11v7s98	1.000000	F	167833	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgtctctaggttgttgtggctgaacgtagcact
+f3v6s37	f11v7s98	1.000000	F	167833	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgtctctaggttgttgtggctgaacgtagcact
+f1v1s10	f1v1s10	1.000000	T	173457	ggatcacacgtctatcactgctcactccaaccccggcccttgacgtccgaggagagggtgcttctgagtatgtatacccaactg
+f1v2s11	f1v1s10	1.000000	F	173457	ggatcacacgtctatcactgctcactccaaccccggcccttgacgtccgaggagagggtgcttctgagtatgtatacccaactg
+f0v7s7	f1v1s10	1.000000	F	173457	ggatcacacgtctatcactgctcactccaaccccggcccttgacgtccgaggagagggtgcttctgagtatgtatacccaactg
+f3v0s31	f3v0s31	1.000000	T	182106	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f4v0s44	f3v0s31	1.000000	F	182106	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f3v3s34	f3v0s31	1.000000	F	182106	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f2v2s20	f2v2s20	1.000000	T	243753	tggactagtagaccgtgtgcctcaatcgacgcggaggacacgttgatttcttatacggcgtctcag
+f6v1s61	f2v2s20	1.000000	F	243753	tggactagtagaccgtgtgcctcaatcgacgcggaggacacgttgatttcttatacggcgtctcag
+f2v3s21	f2v2s20	1.000000	F	243753	tggactagtagaccgtgtgcctcaatcgacgcggaggacacgttgatttcttatacggcgtctcag
+f10v9s86	f10v9s86	1.000000	T	260688	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v7s25	f10v9s86	1.000000	F	260688	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v0s18	f10v9s86	1.000000	F	260688	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f10v3s80	f10v9s86	1.000000	F	260688	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v8s26	f10v9s86	1.000000	F	260688	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag

pkg/obitools/obiclust/testdata/families_default.expected

@@ -0,0 +1,101 @@
+f2v8s26	f2v8s26	1.000000	T	863655	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f10v3s80	f2v8s26	1.000000	F	863655	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v0s18	f2v8s26	1.000000	F	863655	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v7s25	f2v8s26	1.000000	F	863655	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f10v9s86	f2v8s26	1.000000	F	863655	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v3s21	f2v8s26	0.985075	F	863655	tggactagtagaccgtgtgcctcaatcgacgcggaggacacgttgatttcttatacggcgtctcag
+f6v1s61	f2v8s26	0.985075	F	863655	tggactagtagaccgtgtgcctcaatcgacgcggaggacacgttgatttcttatacggcgtctcag
+f2v2s20	f2v8s26	0.985075	F	863655	tggactagtagaccgtgtgcctcaatcgacgcggaggacacgttgatttcttatacggcgtctcag
+f3v3s34	f3v3s34	1.000000	T	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f4v0s44	f3v3s34	1.000000	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f3v0s31	f3v3s34	1.000000	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f0v7s7	f0v7s7	1.000000	T	281628	ggatcacacgtctatcactgctcactccaaccccggcccttgacgtccgaggagagggtgcttctgagtatgtatacccaactg
+f1v2s11	f0v7s7	1.000000	F	281628	ggatcacacgtctatcactgctcactccaaccccggcccttgacgtccgaggagagggtgcttctgagtatgtatacccaactg
+f1v1s10	f0v7s7	1.000000	F	281628	ggatcacacgtctatcactgctcactccaaccccggcccttgacgtccgaggagagggtgcttctgagtatgtatacccaactg
+f3v6s37	f3v3s34	0.935897	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgtctctaggttgttgtggctgaacgtagcact
+f5v0s53	f3v3s34	0.935897	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgtctctaggttgttgtggctgaacgtagcact
+f11v7s98	f3v3s34	0.935897	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgtctctaggttgttgtggctgaacgtagcact
+f2v4s22	f2v8s26	0.970588	F	863655	tggactagtagaccgtgtcgcctcaatcgacgcgtgaggacacgttgattcttatacggcgtctcag
+f10v7s84	f10v7s84	1.000000	T	905994	gtgccggacactcgcaatcttcacaagcagaggtccagctaacacacagcagcatttagtcccgatgggtagc
+f10v0s77	f10v7s84	0.959459	F	905994	ttgccggacactcgcaatcttccaagcagaggtccagctaacacacagcaggcatttagtcccgatgggtagc
+f5v6s59	f2v8s26	0.985075	F	863655	ggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v10s28	f2v8s26	0.985075	F	863655	ggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f1v5s14	f1v5s14	1.000000	T	234004	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f0v4s4	f1v5s14	1.000000	F	234004	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f0v1s1	f1v5s14	1.000000	F	234004	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f0v3s3	f1v5s14	1.000000	F	234004	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f5v3s56	f5v3s56	1.000000	T	192648	ccgcaacgcaccataagatgtaatcactaagaaaaatcggcctaacctgtcatatcgccactt
+f10v2s79	f10v7s84	0.920000	F	905994	ttgccggtcactcgcaatcttaccaaccagaggtccagctaacacacagcaggcatttagtcccgatgggtagc
+f10v13s90	f10v7s84	0.907895	F	905994	tgccggacactcgcaatctccaagcagagagtccaagctaacacacagcaggcatttgtcccgatgggtagc
+f1v4s13	f1v4s13	1.000000	T	304149	gaatcagcttctcaaccaagcgatgcagaaccggctactttaagcattgatgaatgcgtcgtaagtgatactggacgattc
+f10v4s81	f10v7s84	0.933333	F	905994	ttgccggacactggcaatcttccatagcagaggtccagctaacacacagcaggcatttagtcccgatgggtagc
+f10v5s82	f10v7s84	0.945946	F	905994	ttgccggacactcgcaatcttccaagcagaggtccagctaacacatagcaggcatttagtcccgatgggtagc
+f4v8s52	f4v8s52	1.000000	T	359938	ctgatattcgtattgatctactacgtatcaaagtatcccacttttgtgaccccactaagagaaga
+f2v11s29	f2v8s26	0.955882	F	863655	tggactgtagaaccgtgtgcctcaatccacgcgtgaggacacgttgatttcttatacggcgtctcag
+f0v6s6	f1v5s14	0.925000	F	234004	ggatcacagtctacactgctccctccaaccccggcccctggtccgaggagagggtgcttcagagtattataccactg
+f1v3s12	f1v5s14	0.925000	F	234004	ggatcacagtctacactgctccctccaaccccggcccctggtccgaggagagggtgcttcagagtattataccactg
+f0v0s0	f0v7s7	0.916667	F	281628	ggatcacagtctacactgctcactccaaccccggcccctgagtccgaggagagggtgcttcagagtatgtataccactg
+f0v2s2	f0v7s7	0.916667	F	281628	ggatcacagtctacactgctcactccaaccccggcccctgagtccgaggagagggtgcttcagagtatgtataccactg
+f1v7s16	f1v4s13	0.913580	F	304149	gaatcagcttcaaccaagcgatgcagaaccgctgctttaagcatgatgaatcgtcgtaagtgatactcgacgattc
+f2v5s23	f1v4s13	0.913580	F	304149	gaatcagcttcaaccaagcgatgcagaaccgctgctttaagcatgatgaatcgtcgtaagtgatactcgacgattc
+f3v12s43	f3v3s34	0.948718	F	838714	cgaaaaaggtgaatgaaagactgggacgcctcctggtttgggacgctctaggtggttgtggcttgaacgttagcacct
+f8v0s68	f8v0s68	1.000000	T	507278	aagaccttgaacacctctaagcgaaaattggattcgagtcagggaacataaccacgggtgcgt
+f2v1s19	f1v4s13	0.902439	F	304149	gaatcaggttcttccaagcgctgcagaaccggctactttaagcattgatgaatgcgtcagtaagtgatacccgacgattc
+f1v8s17	f1v4s13	0.902439	F	304149	gaatcaggttcttccaagcgctgcagaaccggctactttaagcattgatgaatgcgtcagtaagtgatacccgacgattc
+f10v11s88	f10v7s84	0.933333	F	905994	ttgccggacactcgcaatcttccaagcagaggtccagctaactcacagccaggcatttagtcccgatgggtagc
+f3v5s36	f3v3s34	0.973684	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttatggcttgaaagttagcacct
+f8v7s75	f8v0s68	0.968750	F	507278	aagaccttgaacacctctaagcgaaaattggattccagtcagggaaccataaccacgggtgcgt
+f10v12s89	f10v7s84	0.933333	F	905994	ttgccggacactcgcaatcttccaagcagaggtccagctaacacacacgcaggcatttagacccgatgggtagc
+f4v2s46	f4v8s52	0.938462	F	359938	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagagaaga
+f8v2s70	f8v0s68	0.925373	F	507278	aagaccttgaacaacctctaagccgaaattggaattcgagtcagggaacataaccacgggtgcgat
+f11v8s99	f11v8s99	1.000000	T	421503	agcgttagcaaagagcctggttaatctgccctcgaggatcggtggtgatcagagatgcgggcatccgtttc
+f7v0s64	f7v0s64	1.000000	T	114016	gcttcgtgggaaccagagacaaccgacatatttcgaaccaccgacatacgatccttaaacc
+f11v1s92	f11v8s99	0.944444	F	421503	agcgttagcaaagagcctggttcatcgccctcgaggatcggtggtgatcaagagatgcggcatccgtttc
+f3v2s33	f3v3s34	0.948052	F	838714	cgaaaaaaggtaatgaaaggctgggatgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcact
+f8v3s71	f8v0s68	0.952381	F	507278	aagaccttgaacacctctaagcgaaattggattcgagtcagcgaacataacacgggtgcgt
+f4v3s47	f4v8s52	0.923077	F	359938	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaaagaaga
+f10v10s87	f10v7s84	0.906667	F	905994	tctgccggacactcgcaatcttccaagcagaggtccagctaacacacgcaggcatttatccgatgggtagc
+f11v0s91	f11v8s99	0.985915	F	421503	agcgttagcaaagagcctggttaatcgccctcgaggatcggtggtgatcagagatgcgggcatccgtttc
+f8v5s73	f8v0s68	0.953125	F	507278	aagaccttgtacacctctaagcgataaattggattcgagtcagggaacataaccacggatgcgt
+f8v4s72	f8v0s68	0.984127	F	507278	aagacttgaacacctctaagcgaaaattggattcgagtcagggaacataaccacgggtgcgt
+f3v1s32	f3v3s34	0.974359	F	838714	cgaaaaagagtgaatgaaatggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f3v4s35	f3v3s34	0.948052	F	838714	cgaaaaaggtgaagaaaggctgggacgctcctggttggcgcgctctaggtgttgtggcttgaacgttagcaccta
+f11v6s97	f11v8s99	0.931507	F	421503	agcgttagcaaagaacctggttaatcgccctcgaggatcggtggtggatcggagatgcgggcatcgcgtttc
+f4v1s45	f4v8s52	0.910448	F	359938	ctgtatttcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactatagagaaga
+f0v5s5	f1v5s14	0.925000	F	234004	ggatcacagtctacactgctcactcccccccggcccctgagtccgaggagagggtgcttcaaagtatgtataccactg
+f5v5s58	f5v3s56	0.909091	F	192648	cgcaacgcaccattaagatggtaatcactaaaaaaatcggcctaacctgtccaatcgccactt
+f1v0s9	f1v4s13	0.975309	F	304149	gaatcagcttctaaccaagcgatgcagaaccggctactttaagcattgatgaatgcgtcgtaagtgatactcgacgattc
+f8v6s74	f8v0s68	0.969231	F	507278	aagacccttgaacacctctaagcgaaaattggattcgagtcagggaacataaccacgggtgccgt
+f6v0s60	f6v0s60	1.000000	T	100983	catgtcaagagactggaaccccggtgatgtgaaaaaaggtcttgggtacgtcccatggctacg
+f10v8s85	f10v7s84	0.920000	F	905994	ttgccggacactcgaatcttccaagcagaggtccagctaacacacagcaggcatactagtcccgatgggtagc
+f10v1s78	f10v7s84	0.933333	F	905994	ttgccggacactcgcaatcctccaagcagaggtccagctaacacacagcaggcatttagtcccgatgaggtagc
+f5v4s57	f5v3s56	0.924242	F	192648	cggcaacgcaccataagatggtaatcactaaaaaaatcggcctaacctgtccatatcgccactat
+f3v10s41	f3v3s34	0.948718	F	838714	cgaaaataaggtgaatgaaagggtgggacgctcctagtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f3v7s38	f3v3s34	0.974026	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttcgtgcttgaacgttagcacct
+f10v6s83	f10v7s84	0.932432	F	905994	ttccggacactcgcaatcttccaagcagaggtccagctaacacacagcaggcatttagtcctgatgggtagc
+f11v2s93	f11v8s99	0.958333	F	421503	agcgttagcaaagagcctggttaatcgccctcggaggatcggtggtgatcagagatgcgggcatccgttc
+f3v9s40	f3v3s34	0.986842	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggggttgtggcttgaacgttagcacct
+f11v4s95	f11v8s99	0.944444	F	421503	agcgttagcaaagagcctggttaatcccctcgagatcgggtggtgatcagagatgcgggcatccgtttc
+f8v1s69	f8v0s68	0.984375	F	507278	aagaccttgaacacctctaagcgaaaattggatatcgagtcagggaacataaccacgggtgcgt
+f11v5s96	f11v8s99	0.944444	F	421503	agcgttagcaaagagcctggttaatggccctcgaggatcggtggctgaccagagatgcgggcatccgtttc
+f6v2s62	f6v0s60	0.968254	F	100983	catgtcgagagactggaaccccggtgatgtgaaaaaaggtcttgggtacgtcccatggctac
+f4v6s50	f4v8s52	0.910448	F	359938	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagacgaagag
+f9v0s76	f9v0s76	1.000000	T	29993	gggatcgtggcaagcaacccttgccgcctcgactgcggctaaagacgcatgttccagtaataccta
+f2v12s30	f2v8s26	0.955224	F	863655	tggactagtagaccgtgtgccacaatcgacgctgaggacacgttgatttttatacggcgtctcag
+f11v9s100	f11v8s99	0.972222	F	421503	agcgttagcaaaggagcctggttaatcgccctcgaggatcggtggtgatcagagatgcgggcatccgtttc
+f4v5s49	f4v8s52	0.924242	F	359938	ctatattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagagaagca
+f2v9s27	f2v8s26	0.985075	F	863655	tggactagtagaccgtgtgcctaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f7v3s67	f7v0s64	0.983607	F	114016	gcttcgtgggaccagagacaaccgacatatttcgaaccaccgacatacgatccttaaacc
+f0v8s8	f0v7s7	0.905882	F	281628	ggatcacagtcctacactgctcactccaaccccggccctgagtccgaggagagggtgcttcagagtatgtataccactg
+f2v6s24	f2v8s26	0.940299	F	863655	tggactagtagacgtgtgcctcatcgacgcgtgagacactttgatttcttatacggcgtctcag
+f11v3s94	f11v8s99	0.958333	F	421503	agcgttagcaaagagcctggttaatcgccgtcgaaggatcggtggtgatcagagatgcgggcatccgtttc
+f6v3s63	f6v0s60	0.953846	F	100983	catgtcaagagactggaaccccggtgatgtgaaaaaaggttttgggtcacgtctccatggctacg
+f3v11s42	f3v3s34	0.973684	F	838714	cgaaaaaggtgaatgaaagtctgggacgctcctggtttgggacgctctaggtgttgtggcttgaacgttagcacct
+f4v4s48	f4v8s52	0.923077	F	359938	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagagaaa
+f3v8s39	f3v3s34	0.948052	F	838714	cgaaaaaggtgaatgaaaggcctgggacgctcctggttggggcgctctaggtgtgtggcttgaacgttagacct
+f7v1s65	f7v0s64	0.967742	F	114016	gcttcggggaaccagagacaaccgacatatttcgaaccaccgacatacgatcctttaaacc
+f5v1s54	f5v3s56	0.923077	F	192648	cggaacgcaccataagatggtaatcactaaaaaaatcggcctaacctgtccatatcgccactt
+f4v7s51	f4v7s51	1.000000	T	8599	cgtttattcgtaggatctactacgcatcaaagtatcccacttttgtaccccactaagagcaga
+f7v2s66	f7v0s64	0.951613	F	114016	gcttcgtgggaaccagaacaaccgacatattccgaaccaccggacatacgatccttaaacc
+f1v6s15	f1v4s13	0.950617	F	304149	gaatcagcttctaaccaagcgttgcagaaccggctactttaagcatgatgaatgcgtcgtaagtgatactcgacgattc
+f5v2s55	f5v3s56	0.907692	F	192648	cggcatcgcaccataagatggtaatcactaaaaaaatcggcctaacctgtccatatcgccact

pkg/obitools/obiclust/testdata/families_distance.expected

@@ -0,0 +1,101 @@
+f2v8s26	f2v8s26	0.000000	T	863655	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f10v3s80	f2v8s26	0.000000	F	863655	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v0s18	f2v8s26	0.000000	F	863655	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v7s25	f2v8s26	0.000000	F	863655	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f10v9s86	f2v8s26	0.000000	F	863655	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v3s21	f2v8s26	0.014925	F	863655	tggactagtagaccgtgtgcctcaatcgacgcggaggacacgttgatttcttatacggcgtctcag
+f6v1s61	f2v8s26	0.014925	F	863655	tggactagtagaccgtgtgcctcaatcgacgcggaggacacgttgatttcttatacggcgtctcag
+f2v2s20	f2v8s26	0.014925	F	863655	tggactagtagaccgtgtgcctcaatcgacgcggaggacacgttgatttcttatacggcgtctcag
+f3v3s34	f3v3s34	0.000000	T	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f4v0s44	f3v3s34	0.000000	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f3v0s31	f3v3s34	0.000000	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f0v7s7	f0v7s7	0.000000	T	281628	ggatcacacgtctatcactgctcactccaaccccggcccttgacgtccgaggagagggtgcttctgagtatgtatacccaactg
+f1v2s11	f0v7s7	0.000000	F	281628	ggatcacacgtctatcactgctcactccaaccccggcccttgacgtccgaggagagggtgcttctgagtatgtatacccaactg
+f1v1s10	f0v7s7	0.000000	F	281628	ggatcacacgtctatcactgctcactccaaccccggcccttgacgtccgaggagagggtgcttctgagtatgtatacccaactg
+f3v6s37	f3v3s34	0.064103	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgtctctaggttgttgtggctgaacgtagcact
+f5v0s53	f3v3s34	0.064103	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgtctctaggttgttgtggctgaacgtagcact
+f11v7s98	f3v3s34	0.064103	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgtctctaggttgttgtggctgaacgtagcact
+f2v4s22	f2v8s26	0.029412	F	863655	tggactagtagaccgtgtcgcctcaatcgacgcgtgaggacacgttgattcttatacggcgtctcag
+f10v7s84	f10v7s84	0.000000	T	905994	gtgccggacactcgcaatcttcacaagcagaggtccagctaacacacagcagcatttagtcccgatgggtagc
+f10v0s77	f10v7s84	0.040541	F	905994	ttgccggacactcgcaatcttccaagcagaggtccagctaacacacagcaggcatttagtcccgatgggtagc
+f5v6s59	f2v8s26	0.014925	F	863655	ggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v10s28	f2v8s26	0.014925	F	863655	ggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f1v5s14	f1v5s14	0.000000	T	234004	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f0v4s4	f1v5s14	0.000000	F	234004	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f0v1s1	f1v5s14	0.000000	F	234004	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f0v3s3	f1v5s14	0.000000	F	234004	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f5v3s56	f5v3s56	0.000000	T	192648	ccgcaacgcaccataagatgtaatcactaagaaaaatcggcctaacctgtcatatcgccactt
+f10v2s79	f10v7s84	0.080000	F	905994	ttgccggtcactcgcaatcttaccaaccagaggtccagctaacacacagcaggcatttagtcccgatgggtagc
+f10v13s90	f10v7s84	0.092105	F	905994	tgccggacactcgcaatctccaagcagagagtccaagctaacacacagcaggcatttgtcccgatgggtagc
+f1v4s13	f1v4s13	0.000000	T	304149	gaatcagcttctcaaccaagcgatgcagaaccggctactttaagcattgatgaatgcgtcgtaagtgatactggacgattc
+f10v4s81	f10v7s84	0.066667	F	905994	ttgccggacactggcaatcttccatagcagaggtccagctaacacacagcaggcatttagtcccgatgggtagc
+f10v5s82	f10v7s84	0.054054	F	905994	ttgccggacactcgcaatcttccaagcagaggtccagctaacacatagcaggcatttagtcccgatgggtagc
+f4v8s52	f4v8s52	0.000000	T	359938	ctgatattcgtattgatctactacgtatcaaagtatcccacttttgtgaccccactaagagaaga
+f2v11s29	f2v8s26	0.044118	F	863655	tggactgtagaaccgtgtgcctcaatccacgcgtgaggacacgttgatttcttatacggcgtctcag
+f0v6s6	f1v5s14	0.075000	F	234004	ggatcacagtctacactgctccctccaaccccggcccctggtccgaggagagggtgcttcagagtattataccactg
+f1v3s12	f1v5s14	0.075000	F	234004	ggatcacagtctacactgctccctccaaccccggcccctggtccgaggagagggtgcttcagagtattataccactg
+f0v0s0	f0v7s7	0.083333	F	281628	ggatcacagtctacactgctcactccaaccccggcccctgagtccgaggagagggtgcttcagagtatgtataccactg
+f0v2s2	f0v7s7	0.083333	F	281628	ggatcacagtctacactgctcactccaaccccggcccctgagtccgaggagagggtgcttcagagtatgtataccactg
+f1v7s16	f1v4s13	0.086420	F	304149	gaatcagcttcaaccaagcgatgcagaaccgctgctttaagcatgatgaatcgtcgtaagtgatactcgacgattc
+f2v5s23	f1v4s13	0.086420	F	304149	gaatcagcttcaaccaagcgatgcagaaccgctgctttaagcatgatgaatcgtcgtaagtgatactcgacgattc
+f3v12s43	f3v3s34	0.051282	F	838714	cgaaaaaggtgaatgaaagactgggacgcctcctggtttgggacgctctaggtggttgtggcttgaacgttagcacct
+f8v0s68	f8v0s68	0.000000	T	507278	aagaccttgaacacctctaagcgaaaattggattcgagtcagggaacataaccacgggtgcgt
+f2v1s19	f1v4s13	0.097561	F	304149	gaatcaggttcttccaagcgctgcagaaccggctactttaagcattgatgaatgcgtcagtaagtgatacccgacgattc
+f1v8s17	f1v4s13	0.097561	F	304149	gaatcaggttcttccaagcgctgcagaaccggctactttaagcattgatgaatgcgtcagtaagtgatacccgacgattc
+f10v11s88	f10v7s84	0.066667	F	905994	ttgccggacactcgcaatcttccaagcagaggtccagctaactcacagccaggcatttagtcccgatgggtagc
+f3v5s36	f3v3s34	0.026316	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttatggcttgaaagttagcacct
+f8v7s75	f8v0s68	0.031250	F	507278	aagaccttgaacacctctaagcgaaaattggattccagtcagggaaccataaccacgggtgcgt
+f10v12s89	f10v7s84	0.066667	F	905994	ttgccggacactcgcaatcttccaagcagaggtccagctaacacacacgcaggcatttagacccgatgggtagc
+f4v2s46	f4v8s52	0.061538	F	359938	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagagaaga
+f8v2s70	f8v0s68	0.074627	F	507278	aagaccttgaacaacctctaagccgaaattggaattcgagtcagggaacataaccacgggtgcgat
+f11v8s99	f11v8s99	0.000000	T	421503	agcgttagcaaagagcctggttaatctgccctcgaggatcggtggtgatcagagatgcgggcatccgtttc
+f7v0s64	f7v0s64	0.000000	T	114016	gcttcgtgggaaccagagacaaccgacatatttcgaaccaccgacatacgatccttaaacc
+f11v1s92	f11v8s99	0.055556	F	421503	agcgttagcaaagagcctggttcatcgccctcgaggatcggtggtgatcaagagatgcggcatccgtttc
+f3v2s33	f3v3s34	0.051948	F	838714	cgaaaaaaggtaatgaaaggctgggatgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcact
+f8v3s71	f8v0s68	0.047619	F	507278	aagaccttgaacacctctaagcgaaattggattcgagtcagcgaacataacacgggtgcgt
+f4v3s47	f4v8s52	0.076923	F	359938	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaaagaaga
+f10v10s87	f10v7s84	0.093333	F	905994	tctgccggacactcgcaatcttccaagcagaggtccagctaacacacgcaggcatttatccgatgggtagc
+f11v0s91	f11v8s99	0.014085	F	421503	agcgttagcaaagagcctggttaatcgccctcgaggatcggtggtgatcagagatgcgggcatccgtttc
+f8v5s73	f8v0s68	0.046875	F	507278	aagaccttgtacacctctaagcgataaattggattcgagtcagggaacataaccacggatgcgt
+f8v4s72	f8v0s68	0.015873	F	507278	aagacttgaacacctctaagcgaaaattggattcgagtcagggaacataaccacgggtgcgt
+f3v1s32	f3v3s34	0.025641	F	838714	cgaaaaagagtgaatgaaatggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f3v4s35	f3v3s34	0.051948	F	838714	cgaaaaaggtgaagaaaggctgggacgctcctggttggcgcgctctaggtgttgtggcttgaacgttagcaccta
+f11v6s97	f11v8s99	0.068493	F	421503	agcgttagcaaagaacctggttaatcgccctcgaggatcggtggtggatcggagatgcgggcatcgcgtttc
+f4v1s45	f4v8s52	0.089552	F	359938	ctgtatttcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactatagagaaga
+f0v5s5	f1v5s14	0.075000	F	234004	ggatcacagtctacactgctcactcccccccggcccctgagtccgaggagagggtgcttcaaagtatgtataccactg
+f5v5s58	f5v3s56	0.090909	F	192648	cgcaacgcaccattaagatggtaatcactaaaaaaatcggcctaacctgtccaatcgccactt
+f1v0s9	f1v4s13	0.024691	F	304149	gaatcagcttctaaccaagcgatgcagaaccggctactttaagcattgatgaatgcgtcgtaagtgatactcgacgattc
+f8v6s74	f8v0s68	0.030769	F	507278	aagacccttgaacacctctaagcgaaaattggattcgagtcagggaacataaccacgggtgccgt
+f6v0s60	f6v0s60	0.000000	T	100983	catgtcaagagactggaaccccggtgatgtgaaaaaaggtcttgggtacgtcccatggctacg
+f10v8s85	f10v7s84	0.080000	F	905994	ttgccggacactcgaatcttccaagcagaggtccagctaacacacagcaggcatactagtcccgatgggtagc
+f10v1s78	f10v7s84	0.066667	F	905994	ttgccggacactcgcaatcctccaagcagaggtccagctaacacacagcaggcatttagtcccgatgaggtagc
+f5v4s57	f5v3s56	0.075758	F	192648	cggcaacgcaccataagatggtaatcactaaaaaaatcggcctaacctgtccatatcgccactat
+f3v10s41	f3v3s34	0.051282	F	838714	cgaaaataaggtgaatgaaagggtgggacgctcctagtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f3v7s38	f3v3s34	0.025974	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttcgtgcttgaacgttagcacct
+f10v6s83	f10v7s84	0.067568	F	905994	ttccggacactcgcaatcttccaagcagaggtccagctaacacacagcaggcatttagtcctgatgggtagc
+f11v2s93	f11v8s99	0.041667	F	421503	agcgttagcaaagagcctggttaatcgccctcggaggatcggtggtgatcagagatgcgggcatccgttc
+f3v9s40	f3v3s34	0.013158	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggggttgtggcttgaacgttagcacct
+f11v4s95	f11v8s99	0.055556	F	421503	agcgttagcaaagagcctggttaatcccctcgagatcgggtggtgatcagagatgcgggcatccgtttc
+f8v1s69	f8v0s68	0.015625	F	507278	aagaccttgaacacctctaagcgaaaattggatatcgagtcagggaacataaccacgggtgcgt
+f11v5s96	f11v8s99	0.055556	F	421503	agcgttagcaaagagcctggttaatggccctcgaggatcggtggctgaccagagatgcgggcatccgtttc
+f6v2s62	f6v0s60	0.031746	F	100983	catgtcgagagactggaaccccggtgatgtgaaaaaaggtcttgggtacgtcccatggctac
+f4v6s50	f4v8s52	0.089552	F	359938	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagacgaagag
+f9v0s76	f9v0s76	0.000000	T	29993	gggatcgtggcaagcaacccttgccgcctcgactgcggctaaagacgcatgttccagtaataccta
+f2v12s30	f2v8s26	0.044776	F	863655	tggactagtagaccgtgtgccacaatcgacgctgaggacacgttgatttttatacggcgtctcag
+f11v9s100	f11v8s99	0.027778	F	421503	agcgttagcaaaggagcctggttaatcgccctcgaggatcggtggtgatcagagatgcgggcatccgtttc
+f4v5s49	f4v8s52	0.075758	F	359938	ctatattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagagaagca
+f2v9s27	f2v8s26	0.014925	F	863655	tggactagtagaccgtgtgcctaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f7v3s67	f7v0s64	0.016393	F	114016	gcttcgtgggaccagagacaaccgacatatttcgaaccaccgacatacgatccttaaacc
+f0v8s8	f0v7s7	0.094118	F	281628	ggatcacagtcctacactgctcactccaaccccggccctgagtccgaggagagggtgcttcagagtatgtataccactg
+f2v6s24	f2v8s26	0.059701	F	863655	tggactagtagacgtgtgcctcatcgacgcgtgagacactttgatttcttatacggcgtctcag
+f11v3s94	f11v8s99	0.041667	F	421503	agcgttagcaaagagcctggttaatcgccgtcgaaggatcggtggtgatcagagatgcgggcatccgtttc
+f6v3s63	f6v0s60	0.046154	F	100983	catgtcaagagactggaaccccggtgatgtgaaaaaaggttttgggtcacgtctccatggctacg
+f3v11s42	f3v3s34	0.026316	F	838714	cgaaaaaggtgaatgaaagtctgggacgctcctggtttgggacgctctaggtgttgtggcttgaacgttagcacct
+f4v4s48	f4v8s52	0.076923	F	359938	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagagaaa
+f3v8s39	f3v3s34	0.051948	F	838714	cgaaaaaggtgaatgaaaggcctgggacgctcctggttggggcgctctaggtgtgtggcttgaacgttagacct
+f7v1s65	f7v0s64	0.032258	F	114016	gcttcggggaaccagagacaaccgacatatttcgaaccaccgacatacgatcctttaaacc
+f5v1s54	f5v3s56	0.076923	F	192648	cggaacgcaccataagatggtaatcactaaaaaaatcggcctaacctgtccatatcgccactt
+f4v7s51	f4v7s51	0.000000	T	8599	cgtttattcgtaggatctactacgcatcaaagtatcccacttttgtaccccactaagagcaga
+f7v2s66	f7v0s64	0.048387	F	114016	gcttcgtgggaaccagaacaaccgacatattccgaaccaccggacatacgatccttaaacc
+f1v6s15	f1v4s13	0.049383	F	304149	gaatcagcttctaaccaagcgttgcagaaccggctactttaagcatgatgaatgcgtcgtaagtgatactcgacgattc
+f5v2s55	f5v3s56	0.092308	F	192648	cggcatcgcaccataagatggtaatcactaaaaaaatcggcctaacctgtccatatcgccact

pkg/obitools/obiclust/testdata/families_exact.expected

@@ -0,0 +1,101 @@
+f2v8s26	f2v8s26	1.000000	T	863655	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f10v3s80	f2v8s26	1.000000	F	863655	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v0s18	f2v8s26	1.000000	F	863655	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v7s25	f2v8s26	1.000000	F	863655	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f10v9s86	f2v8s26	1.000000	F	863655	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v3s21	f2v8s26	0.985075	F	863655	tggactagtagaccgtgtgcctcaatcgacgcggaggacacgttgatttcttatacggcgtctcag
+f6v1s61	f2v8s26	0.985075	F	863655	tggactagtagaccgtgtgcctcaatcgacgcggaggacacgttgatttcttatacggcgtctcag
+f2v2s20	f2v8s26	0.985075	F	863655	tggactagtagaccgtgtgcctcaatcgacgcggaggacacgttgatttcttatacggcgtctcag
+f3v3s34	f3v3s34	1.000000	T	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f4v0s44	f3v3s34	1.000000	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f3v0s31	f3v3s34	1.000000	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f0v7s7	f0v7s7	1.000000	T	173457	ggatcacacgtctatcactgctcactccaaccccggcccttgacgtccgaggagagggtgcttctgagtatgtatacccaactg
+f1v2s11	f0v7s7	1.000000	F	173457	ggatcacacgtctatcactgctcactccaaccccggcccttgacgtccgaggagagggtgcttctgagtatgtatacccaactg
+f1v1s10	f0v7s7	1.000000	F	173457	ggatcacacgtctatcactgctcactccaaccccggcccttgacgtccgaggagagggtgcttctgagtatgtatacccaactg
+f3v6s37	f3v3s34	0.935897	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgtctctaggttgttgtggctgaacgtagcact
+f5v0s53	f3v3s34	0.935897	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgtctctaggttgttgtggctgaacgtagcact
+f11v7s98	f3v3s34	0.935897	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgtctctaggttgttgtggctgaacgtagcact
+f2v4s22	f2v8s26	0.970588	F	863655	tggactagtagaccgtgtcgcctcaatcgacgcgtgaggacacgttgattcttatacggcgtctcag
+f10v7s84	f10v7s84	1.000000	T	905994	gtgccggacactcgcaatcttcacaagcagaggtccagctaacacacagcagcatttagtcccgatgggtagc
+f10v0s77	f10v7s84	0.959459	F	905994	ttgccggacactcgcaatcttccaagcagaggtccagctaacacacagcaggcatttagtcccgatgggtagc
+f5v6s59	f2v8s26	0.985075	F	863655	ggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v10s28	f2v8s26	0.985075	F	863655	ggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f1v5s14	f1v5s14	1.000000	T	342175	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f0v4s4	f1v5s14	1.000000	F	342175	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f0v1s1	f1v5s14	1.000000	F	342175	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f0v3s3	f1v5s14	1.000000	F	342175	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f5v3s56	f5v3s56	1.000000	T	192648	ccgcaacgcaccataagatgtaatcactaagaaaaatcggcctaacctgtcatatcgccactt
+f10v2s79	f10v7s84	0.920000	F	905994	ttgccggtcactcgcaatcttaccaaccagaggtccagctaacacacagcaggcatttagtcccgatgggtagc
+f10v13s90	f10v7s84	0.907895	F	905994	tgccggacactcgcaatctccaagcagagagtccaagctaacacacagcaggcatttgtcccgatgggtagc
+f1v4s13	f1v4s13	1.000000	T	304149	gaatcagcttctcaaccaagcgatgcagaaccggctactttaagcattgatgaatgcgtcgtaagtgatactggacgattc
+f10v4s81	f10v7s84	0.933333	F	905994	ttgccggacactggcaatcttccatagcagaggtccagctaacacacagcaggcatttagtcccgatgggtagc
+f10v5s82	f10v7s84	0.945946	F	905994	ttgccggacactcgcaatcttccaagcagaggtccagctaacacatagcaggcatttagtcccgatgggtagc
+f4v8s52	f4v8s52	1.000000	T	359938	ctgatattcgtattgatctactacgtatcaaagtatcccacttttgtgaccccactaagagaaga
+f2v11s29	f2v8s26	0.955882	F	863655	tggactgtagaaccgtgtgcctcaatccacgcgtgaggacacgttgatttcttatacggcgtctcag
+f0v6s6	f1v5s14	0.925000	F	342175	ggatcacagtctacactgctccctccaaccccggcccctggtccgaggagagggtgcttcagagtattataccactg
+f1v3s12	f1v5s14	0.925000	F	342175	ggatcacagtctacactgctccctccaaccccggcccctggtccgaggagagggtgcttcagagtattataccactg
+f0v0s0	f1v5s14	0.962500	F	342175	ggatcacagtctacactgctcactccaaccccggcccctgagtccgaggagagggtgcttcagagtatgtataccactg
+f0v2s2	f1v5s14	0.962500	F	342175	ggatcacagtctacactgctcactccaaccccggcccctgagtccgaggagagggtgcttcagagtatgtataccactg
+f1v7s16	f1v4s13	0.913580	F	304149	gaatcagcttcaaccaagcgatgcagaaccgctgctttaagcatgatgaatcgtcgtaagtgatactcgacgattc
+f2v5s23	f1v4s13	0.913580	F	304149	gaatcagcttcaaccaagcgatgcagaaccgctgctttaagcatgatgaatcgtcgtaagtgatactcgacgattc
+f3v12s43	f3v3s34	0.948718	F	838714	cgaaaaaggtgaatgaaagactgggacgcctcctggtttgggacgctctaggtggttgtggcttgaacgttagcacct
+f8v0s68	f8v0s68	1.000000	T	507278	aagaccttgaacacctctaagcgaaaattggattcgagtcagggaacataaccacgggtgcgt
+f2v1s19	f1v4s13	0.902439	F	304149	gaatcaggttcttccaagcgctgcagaaccggctactttaagcattgatgaatgcgtcagtaagtgatacccgacgattc
+f1v8s17	f1v4s13	0.902439	F	304149	gaatcaggttcttccaagcgctgcagaaccggctactttaagcattgatgaatgcgtcagtaagtgatacccgacgattc
+f10v11s88	f10v7s84	0.933333	F	905994	ttgccggacactcgcaatcttccaagcagaggtccagctaactcacagccaggcatttagtcccgatgggtagc
+f3v5s36	f3v3s34	0.973684	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttatggcttgaaagttagcacct
+f8v7s75	f8v0s68	0.968750	F	507278	aagaccttgaacacctctaagcgaaaattggattccagtcagggaaccataaccacgggtgcgt
+f10v12s89	f10v7s84	0.933333	F	905994	ttgccggacactcgcaatcttccaagcagaggtccagctaacacacacgcaggcatttagacccgatgggtagc
+f4v2s46	f4v8s52	0.938462	F	359938	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagagaaga
+f8v2s70	f8v0s68	0.925373	F	507278	aagaccttgaacaacctctaagccgaaattggaattcgagtcagggaacataaccacgggtgcgat
+f11v8s99	f11v8s99	1.000000	T	421503	agcgttagcaaagagcctggttaatctgccctcgaggatcggtggtgatcagagatgcgggcatccgtttc
+f7v0s64	f7v0s64	1.000000	T	114016	gcttcgtgggaaccagagacaaccgacatatttcgaaccaccgacatacgatccttaaacc
+f11v1s92	f11v8s99	0.944444	F	421503	agcgttagcaaagagcctggttcatcgccctcgaggatcggtggtgatcaagagatgcggcatccgtttc
+f3v2s33	f3v3s34	0.948052	F	838714	cgaaaaaaggtaatgaaaggctgggatgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcact
+f8v3s71	f8v0s68	0.952381	F	507278	aagaccttgaacacctctaagcgaaattggattcgagtcagcgaacataacacgggtgcgt
+f4v3s47	f4v8s52	0.923077	F	359938	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaaagaaga
+f10v10s87	f10v7s84	0.906667	F	905994	tctgccggacactcgcaatcttccaagcagaggtccagctaacacacgcaggcatttatccgatgggtagc
+f11v0s91	f11v8s99	0.985915	F	421503	agcgttagcaaagagcctggttaatcgccctcgaggatcggtggtgatcagagatgcgggcatccgtttc
+f8v5s73	f8v0s68	0.953125	F	507278	aagaccttgtacacctctaagcgataaattggattcgagtcagggaacataaccacggatgcgt
+f8v4s72	f8v0s68	0.984127	F	507278	aagacttgaacacctctaagcgaaaattggattcgagtcagggaacataaccacgggtgcgt
+f3v1s32	f3v3s34	0.974359	F	838714	cgaaaaagagtgaatgaaatggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f3v4s35	f3v3s34	0.948052	F	838714	cgaaaaaggtgaagaaaggctgggacgctcctggttggcgcgctctaggtgttgtggcttgaacgttagcaccta
+f11v6s97	f11v8s99	0.931507	F	421503	agcgttagcaaagaacctggttaatcgccctcgaggatcggtggtggatcggagatgcgggcatcgcgtttc
+f4v1s45	f4v8s52	0.910448	F	359938	ctgtatttcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactatagagaaga
+f0v5s5	f1v5s14	0.925000	F	342175	ggatcacagtctacactgctcactcccccccggcccctgagtccgaggagagggtgcttcaaagtatgtataccactg
+f5v5s58	f5v3s56	0.909091	F	192648	cgcaacgcaccattaagatggtaatcactaaaaaaatcggcctaacctgtccaatcgccactt
+f1v0s9	f1v4s13	0.975309	F	304149	gaatcagcttctaaccaagcgatgcagaaccggctactttaagcattgatgaatgcgtcgtaagtgatactcgacgattc
+f8v6s74	f8v0s68	0.969231	F	507278	aagacccttgaacacctctaagcgaaaattggattcgagtcagggaacataaccacgggtgccgt
+f6v0s60	f6v0s60	1.000000	T	100983	catgtcaagagactggaaccccggtgatgtgaaaaaaggtcttgggtacgtcccatggctacg
+f10v8s85	f10v7s84	0.920000	F	905994	ttgccggacactcgaatcttccaagcagaggtccagctaacacacagcaggcatactagtcccgatgggtagc
+f10v1s78	f10v7s84	0.933333	F	905994	ttgccggacactcgcaatcctccaagcagaggtccagctaacacacagcaggcatttagtcccgatgaggtagc
+f5v4s57	f5v3s56	0.924242	F	192648	cggcaacgcaccataagatggtaatcactaaaaaaatcggcctaacctgtccatatcgccactat
+f3v10s41	f3v3s34	0.948718	F	838714	cgaaaataaggtgaatgaaagggtgggacgctcctagtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f3v7s38	f3v3s34	0.974026	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttcgtgcttgaacgttagcacct
+f10v6s83	f10v7s84	0.932432	F	905994	ttccggacactcgcaatcttccaagcagaggtccagctaacacacagcaggcatttagtcctgatgggtagc
+f11v2s93	f11v8s99	0.958333	F	421503	agcgttagcaaagagcctggttaatcgccctcggaggatcggtggtgatcagagatgcgggcatccgttc
+f3v9s40	f3v3s34	0.986842	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggggttgtggcttgaacgttagcacct
+f11v4s95	f11v8s99	0.944444	F	421503	agcgttagcaaagagcctggttaatcccctcgagatcgggtggtgatcagagatgcgggcatccgtttc
+f8v1s69	f8v0s68	0.984375	F	507278	aagaccttgaacacctctaagcgaaaattggatatcgagtcagggaacataaccacgggtgcgt
+f11v5s96	f11v8s99	0.944444	F	421503	agcgttagcaaagagcctggttaatggccctcgaggatcggtggctgaccagagatgcgggcatccgtttc
+f6v2s62	f6v0s60	0.968254	F	100983	catgtcgagagactggaaccccggtgatgtgaaaaaaggtcttgggtacgtcccatggctac
+f4v6s50	f4v8s52	0.910448	F	359938	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagacgaagag
+f9v0s76	f9v0s76	1.000000	T	29993	gggatcgtggcaagcaacccttgccgcctcgactgcggctaaagacgcatgttccagtaataccta
+f2v12s30	f2v8s26	0.955224	F	863655	tggactagtagaccgtgtgccacaatcgacgctgaggacacgttgatttttatacggcgtctcag
+f11v9s100	f11v8s99	0.972222	F	421503	agcgttagcaaaggagcctggttaatcgccctcgaggatcggtggtgatcagagatgcgggcatccgtttc
+f4v5s49	f4v8s52	0.924242	F	359938	ctatattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagagaagca
+f2v9s27	f2v8s26	0.985075	F	863655	tggactagtagaccgtgtgcctaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f7v3s67	f7v0s64	0.983607	F	114016	gcttcgtgggaccagagacaaccgacatatttcgaaccaccgacatacgatccttaaacc
+f0v8s8	f1v5s14	0.950000	F	342175	ggatcacagtcctacactgctcactccaaccccggccctgagtccgaggagagggtgcttcagagtatgtataccactg
+f2v6s24	f2v8s26	0.940299	F	863655	tggactagtagacgtgtgcctcatcgacgcgtgagacactttgatttcttatacggcgtctcag
+f11v3s94	f11v8s99	0.958333	F	421503	agcgttagcaaagagcctggttaatcgccgtcgaaggatcggtggtgatcagagatgcgggcatccgtttc
+f6v3s63	f6v0s60	0.953846	F	100983	catgtcaagagactggaaccccggtgatgtgaaaaaaggttttgggtcacgtctccatggctacg
+f3v11s42	f3v3s34	0.973684	F	838714	cgaaaaaggtgaatgaaagtctgggacgctcctggtttgggacgctctaggtgttgtggcttgaacgttagcacct
+f4v4s48	f4v8s52	0.923077	F	359938	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagagaaa
+f3v8s39	f3v3s34	0.948052	F	838714	cgaaaaaggtgaatgaaaggcctgggacgctcctggttggggcgctctaggtgtgtggcttgaacgttagacct
+f7v1s65	f7v0s64	0.967742	F	114016	gcttcggggaaccagagacaaccgacatatttcgaaccaccgacatacgatcctttaaacc
+f5v1s54	f5v3s56	0.923077	F	192648	cggaacgcaccataagatggtaatcactaaaaaaatcggcctaacctgtccatatcgccactt
+f4v7s51	f4v7s51	1.000000	T	8599	cgtttattcgtaggatctactacgcatcaaagtatcccacttttgtaccccactaagagcaga
+f7v2s66	f7v0s64	0.951613	F	114016	gcttcgtgggaaccagaacaaccgacatattccgaaccaccggacatacgatccttaaacc
+f1v6s15	f1v4s13	0.950617	F	304149	gaatcagcttctaaccaagcgttgcagaaccggctactttaagcatgatgaatgcgtcgtaagtgatactcgacgattc
+f5v2s55	f5v3s56	0.907692	F	192648	cggcatcgcaccataagatggtaatcactaaaaaaatcggcctaacctgtccatatcgccact

pkg/obitools/obiclust/testdata/families_longest.expected

@@ -0,0 +1,101 @@
+f2v8s26	f2v8s26	1.000000	T	863655	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f10v3s80	f2v8s26	1.000000	F	863655	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v0s18	f2v8s26	1.000000	F	863655	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v7s25	f2v8s26	1.000000	F	863655	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f10v9s86	f2v8s26	1.000000	F	863655	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v3s21	f2v8s26	0.985075	F	863655	tggactagtagaccgtgtgcctcaatcgacgcggaggacacgttgatttcttatacggcgtctcag
+f6v1s61	f2v8s26	0.985075	F	863655	tggactagtagaccgtgtgcctcaatcgacgcggaggacacgttgatttcttatacggcgtctcag
+f2v2s20	f2v8s26	0.985075	F	863655	tggactagtagaccgtgtgcctcaatcgacgcggaggacacgttgatttcttatacggcgtctcag
+f3v3s34	f3v3s34	1.000000	T	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f4v0s44	f3v3s34	1.000000	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f3v0s31	f3v3s34	1.000000	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f0v7s7	f0v7s7	1.000000	T	515632	ggatcacacgtctatcactgctcactccaaccccggcccttgacgtccgaggagagggtgcttctgagtatgtatacccaactg
+f1v2s11	f0v7s7	1.000000	F	515632	ggatcacacgtctatcactgctcactccaaccccggcccttgacgtccgaggagagggtgcttctgagtatgtatacccaactg
+f1v1s10	f0v7s7	1.000000	F	515632	ggatcacacgtctatcactgctcactccaaccccggcccttgacgtccgaggagagggtgcttctgagtatgtatacccaactg
+f3v6s37	f3v3s34	0.960526	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgtctctaggttgttgtggctgaacgtagcact
+f5v0s53	f3v3s34	0.960526	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgtctctaggttgttgtggctgaacgtagcact
+f11v7s98	f3v3s34	0.960526	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgtctctaggttgttgtggctgaacgtagcact
+f2v4s22	f2v8s26	0.985075	F	863655	tggactagtagaccgtgtcgcctcaatcgacgcgtgaggacacgttgattcttatacggcgtctcag
+f10v7s84	f10v7s84	1.000000	T	905994	gtgccggacactcgcaatcttcacaagcagaggtccagctaacacacagcagcatttagtcccgatgggtagc
+f10v0s77	f10v7s84	0.972603	F	905994	ttgccggacactcgcaatcttccaagcagaggtccagctaacacacagcaggcatttagtcccgatgggtagc
+f5v6s59	f2v8s26	0.985075	F	863655	ggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v10s28	f2v8s26	0.985075	F	863655	ggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f1v5s14	f0v7s7	0.892857	F	515632	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f0v4s4	f0v7s7	0.892857	F	515632	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f0v1s1	f0v7s7	0.892857	F	515632	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f0v3s3	f0v7s7	0.892857	F	515632	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f5v3s56	f5v3s56	1.000000	T	192648	ccgcaacgcaccataagatgtaatcactaagaaaaatcggcctaacctgtcatatcgccactt
+f10v2s79	f10v7s84	0.932432	F	905994	ttgccggtcactcgcaatcttaccaaccagaggtccagctaacacacagcaggcatttagtcccgatgggtagc
+f10v13s90	f10v7s84	0.945205	F	905994	tgccggacactcgcaatctccaagcagagagtccaagctaacacacagcaggcatttgtcccgatgggtagc
+f1v4s13	f1v4s13	1.000000	T	304149	gaatcagcttctcaaccaagcgatgcagaaccggctactttaagcattgatgaatgcgtcgtaagtgatactggacgattc
+f10v4s81	f10v7s84	0.945946	F	905994	ttgccggacactggcaatcttccatagcagaggtccagctaacacacagcaggcatttagtcccgatgggtagc
+f10v5s82	f10v7s84	0.958904	F	905994	ttgccggacactcgcaatcttccaagcagaggtccagctaacacatagcaggcatttagtcccgatgggtagc
+f4v8s52	f4v8s52	1.000000	T	368537	ctgatattcgtattgatctactacgtatcaaagtatcccacttttgtgaccccactaagagaaga
+f2v11s29	f2v8s26	0.970149	F	863655	tggactgtagaaccgtgtgcctcaatccacgcgtgaggacacgttgatttcttatacggcgtctcag
+f0v6s6	f0v7s7	0.880952	F	515632	ggatcacagtctacactgctccctccaaccccggcccctggtccgaggagagggtgcttcagagtattataccactg
+f1v3s12	f0v7s7	0.880952	F	515632	ggatcacagtctacactgctccctccaaccccggcccctggtccgaggagagggtgcttcagagtattataccactg
+f0v0s0	f0v7s7	0.916667	F	515632	ggatcacagtctacactgctcactccaaccccggcccctgagtccgaggagagggtgcttcagagtatgtataccactg
+f0v2s2	f0v7s7	0.916667	F	515632	ggatcacagtctacactgctcactccaaccccggcccctgagtccgaggagagggtgcttcagagtatgtataccactg
+f1v7s16	f1v4s13	0.913580	F	304149	gaatcagcttcaaccaagcgatgcagaaccgctgctttaagcatgatgaatcgtcgtaagtgatactcgacgattc
+f2v5s23	f1v4s13	0.913580	F	304149	gaatcagcttcaaccaagcgatgcagaaccgctgctttaagcatgatgaatcgtcgtaagtgatactcgacgattc
+f3v12s43	f3v3s34	0.948718	F	838714	cgaaaaaggtgaatgaaagactgggacgcctcctggtttgggacgctctaggtggttgtggcttgaacgttagcacct
+f8v0s68	f8v0s68	1.000000	T	507278	aagaccttgaacacctctaagcgaaaattggattcgagtcagggaacataaccacgggtgcgt
+f2v1s19	f1v4s13	0.913580	F	304149	gaatcaggttcttccaagcgctgcagaaccggctactttaagcattgatgaatgcgtcagtaagtgatacccgacgattc
+f1v8s17	f1v4s13	0.913580	F	304149	gaatcaggttcttccaagcgctgcagaaccggctactttaagcattgatgaatgcgtcagtaagtgatacccgacgattc
+f10v11s88	f10v7s84	0.945946	F	905994	ttgccggacactcgcaatcttccaagcagaggtccagctaactcacagccaggcatttagtcccgatgggtagc
+f3v5s36	f3v3s34	0.973684	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttatggcttgaaagttagcacct
+f8v7s75	f8v0s68	0.968750	F	507278	aagaccttgaacacctctaagcgaaaattggattccagtcagggaaccataaccacgggtgcgt
+f10v12s89	f10v7s84	0.945946	F	905994	ttgccggacactcgcaatcttccaagcagaggtccagctaacacacacgcaggcatttagacccgatgggtagc
+f4v2s46	f4v8s52	0.938462	F	368537	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagagaaga
+f8v2s70	f8v0s68	0.939394	F	507278	aagaccttgaacaacctctaagccgaaattggaattcgagtcagggaacataaccacgggtgcgat
+f11v8s99	f11v8s99	1.000000	T	421503	agcgttagcaaagagcctggttaatctgccctcgaggatcggtggtgatcagagatgcgggcatccgtttc
+f7v0s64	f7v0s64	1.000000	T	114016	gcttcgtgggaaccagagacaaccgacatatttcgaaccaccgacatacgatccttaaacc
+f11v1s92	f11v8s99	0.957746	F	421503	agcgttagcaaagagcctggttcatcgccctcgaggatcggtggtgatcaagagatgcggcatccgtttc
+f3v2s33	f3v3s34	0.960526	F	838714	cgaaaaaaggtaatgaaaggctgggatgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcact
+f8v3s71	f8v0s68	0.952381	F	507278	aagaccttgaacacctctaagcgaaattggattcgagtcagcgaacataacacgggtgcgt
+f4v3s47	f4v8s52	0.923077	F	368537	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaaagaaga
+f10v10s87	f10v7s84	0.931507	F	905994	tctgccggacactcgcaatcttccaagcagaggtccagctaacacacgcaggcatttatccgatgggtagc
+f11v0s91	f11v8s99	0.985915	F	421503	agcgttagcaaagagcctggttaatcgccctcgaggatcggtggtgatcagagatgcgggcatccgtttc
+f8v5s73	f8v0s68	0.953125	F	507278	aagaccttgtacacctctaagcgataaattggattcgagtcagggaacataaccacggatgcgt
+f8v4s72	f8v0s68	0.984127	F	507278	aagacttgaacacctctaagcgaaaattggattcgagtcagggaacataaccacgggtgcgt
+f3v1s32	f3v3s34	0.974359	F	838714	cgaaaaagagtgaatgaaatggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f3v4s35	f3v3s34	0.960526	F	838714	cgaaaaaggtgaagaaaggctgggacgctcctggttggcgcgctctaggtgttgtggcttgaacgttagcaccta
+f11v6s97	f11v8s99	0.944444	F	421503	agcgttagcaaagaacctggttaatcgccctcgaggatcggtggtggatcggagatgcgggcatcgcgtttc
+f4v1s45	f4v8s52	0.938462	F	368537	ctgtatttcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactatagagaaga
+f0v5s5	f0v7s7	0.880952	F	515632	ggatcacagtctacactgctcactcccccccggcccctgagtccgaggagagggtgcttcaaagtatgtataccactg
+f5v5s58	f5v3s56	0.952381	F	192648	cgcaacgcaccattaagatggtaatcactaaaaaaatcggcctaacctgtccaatcgccactt
+f1v0s9	f1v4s13	0.975309	F	304149	gaatcagcttctaaccaagcgatgcagaaccggctactttaagcattgatgaatgcgtcgtaagtgatactcgacgattc
+f8v6s74	f8v0s68	0.969231	F	507278	aagacccttgaacacctctaagcgaaaattggattcgagtcagggaacataaccacgggtgccgt
+f6v0s60	f6v0s60	1.000000	T	100983	catgtcaagagactggaaccccggtgatgtgaaaaaaggtcttgggtacgtcccatggctacg
+f10v8s85	f10v7s84	0.945205	F	905994	ttgccggacactcgaatcttccaagcagaggtccagctaacacacagcaggcatactagtcccgatgggtagc
+f10v1s78	f10v7s84	0.945946	F	905994	ttgccggacactcgcaatcctccaagcagaggtccagctaacacacagcaggcatttagtcccgatgaggtagc
+f5v4s57	f5v3s56	0.938462	F	192648	cggcaacgcaccataagatggtaatcactaaaaaaatcggcctaacctgtccatatcgccactat
+f3v10s41	f3v3s34	0.948718	F	838714	cgaaaataaggtgaatgaaagggtgggacgctcctagtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f3v7s38	f3v3s34	0.986842	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttcgtgcttgaacgttagcacct
+f10v6s83	f10v7s84	0.945205	F	905994	ttccggacactcgcaatcttccaagcagaggtccagctaacacacagcaggcatttagtcctgatgggtagc
+f11v2s93	f11v8s99	0.971831	F	421503	agcgttagcaaagagcctggttaatcgccctcggaggatcggtggtgatcagagatgcgggcatccgttc
+f3v9s40	f3v3s34	0.986842	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggggttgtggcttgaacgttagcacct
+f11v4s95	f11v8s99	0.957746	F	421503	agcgttagcaaagagcctggttaatcccctcgagatcgggtggtgatcagagatgcgggcatccgtttc
+f8v1s69	f8v0s68	0.984375	F	507278	aagaccttgaacacctctaagcgaaaattggatatcgagtcagggaacataaccacgggtgcgt
+f11v5s96	f11v8s99	0.957746	F	421503	agcgttagcaaagagcctggttaatggccctcgaggatcggtggctgaccagagatgcgggcatccgtttc
+f6v2s62	f6v0s60	0.968254	F	100983	catgtcgagagactggaaccccggtgatgtgaaaaaaggtcttgggtacgtcccatggctac
+f4v6s50	f4v8s52	0.938462	F	368537	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagacgaagag
+f9v0s76	f9v0s76	1.000000	T	29993	gggatcgtggcaagcaacccttgccgcctcgactgcggctaaagacgcatgttccagtaataccta
+f2v12s30	f2v8s26	0.955224	F	863655	tggactagtagaccgtgtgccacaatcgacgctgaggacacgttgatttttatacggcgtctcag
+f11v9s100	f11v8s99	0.985915	F	421503	agcgttagcaaaggagcctggttaatcgccctcgaggatcggtggtgatcagagatgcgggcatccgtttc
+f4v5s49	f4v8s52	0.938462	F	368537	ctatattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagagaagca
+f2v9s27	f2v8s26	0.985075	F	863655	tggactagtagaccgtgtgcctaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f7v3s67	f7v0s64	0.983607	F	114016	gcttcgtgggaccagagacaaccgacatatttcgaaccaccgacatacgatccttaaacc
+f0v8s8	f0v7s7	0.916667	F	515632	ggatcacagtcctacactgctcactccaaccccggccctgagtccgaggagagggtgcttcagagtatgtataccactg
+f2v6s24	f2v8s26	0.940299	F	863655	tggactagtagacgtgtgcctcatcgacgcgtgagacactttgatttcttatacggcgtctcag
+f11v3s94	f11v8s99	0.971831	F	421503	agcgttagcaaagagcctggttaatcgccgtcgaaggatcggtggtgatcagagatgcgggcatccgtttc
+f6v3s63	f6v0s60	0.953846	F	100983	catgtcaagagactggaaccccggtgatgtgaaaaaaggttttgggtcacgtctccatggctacg
+f3v11s42	f3v3s34	0.973684	F	838714	cgaaaaaggtgaatgaaagtctgggacgctcctggtttgggacgctctaggtgttgtggcttgaacgttagcacct
+f4v4s48	f4v8s52	0.923077	F	368537	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagagaaa
+f3v8s39	f3v3s34	0.960526	F	838714	cgaaaaaggtgaatgaaaggcctgggacgctcctggttggggcgctctaggtgtgtggcttgaacgttagacct
+f7v1s65	f7v0s64	0.983607	F	114016	gcttcggggaaccagagacaaccgacatatttcgaaccaccgacatacgatcctttaaacc
+f5v1s54	f5v3s56	0.952381	F	192648	cggaacgcaccataagatggtaatcactaaaaaaatcggcctaacctgtccatatcgccactt
+f4v7s51	f4v8s52	0.892308	F	368537	cgtttattcgtaggatctactacgcatcaaagtatcccacttttgtaccccactaagagcaga
+f7v2s66	f7v0s64	0.967213	F	114016	gcttcgtgggaaccagaacaaccgacatattccgaaccaccggacatacgatccttaaacc
+f1v6s15	f1v4s13	0.950617	F	304149	gaatcagcttctaaccaagcgttgcagaaccggctactttaagcatgatgaatgcgtcgtaagtgatactcgacgattc
+f5v2s55	f5v3s56	0.936508	F	192648	cggcatcgcaccataagatggtaatcactaaaaaaatcggcctaacctgtccatatcgccact

pkg/obitools/obiclust/testdata/families_ratio.expected

@@ -0,0 +1,101 @@
+f2v8s26	f2v8s26	1.000000	T	619902	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f10v3s80	f2v8s26	1.000000	F	619902	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v0s18	f2v8s26	1.000000	F	619902	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v7s25	f2v8s26	1.000000	F	619902	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f10v9s86	f2v8s26	1.000000	F	619902	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v3s21	f2v3s21	1.000000	T	243753	tggactagtagaccgtgtgcctcaatcgacgcggaggacacgttgatttcttatacggcgtctcag
+f6v1s61	f2v3s21	1.000000	F	243753	tggactagtagaccgtgtgcctcaatcgacgcggaggacacgttgatttcttatacggcgtctcag
+f2v2s20	f2v3s21	1.000000	F	243753	tggactagtagaccgtgtgcctcaatcgacgcggaggacacgttgatttcttatacggcgtctcag
+f3v3s34	f3v3s34	1.000000	T	670881	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f4v0s44	f3v3s34	1.000000	F	670881	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f3v0s31	f3v3s34	1.000000	F	670881	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f0v7s7	f0v7s7	1.000000	T	281628	ggatcacacgtctatcactgctcactccaaccccggcccttgacgtccgaggagagggtgcttctgagtatgtatacccaactg
+f1v2s11	f0v7s7	1.000000	F	281628	ggatcacacgtctatcactgctcactccaaccccggcccttgacgtccgaggagagggtgcttctgagtatgtatacccaactg
+f1v1s10	f0v7s7	1.000000	F	281628	ggatcacacgtctatcactgctcactccaaccccggcccttgacgtccgaggagagggtgcttctgagtatgtatacccaactg
+f3v6s37	f3v6s37	1.000000	T	167833	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgtctctaggttgttgtggctgaacgtagcact
+f5v0s53	f3v6s37	1.000000	F	167833	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgtctctaggttgttgtggctgaacgtagcact
+f11v7s98	f3v6s37	1.000000	F	167833	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgtctctaggttgttgtggctgaacgtagcact
+f2v4s22	f2v8s26	0.970588	F	619902	tggactagtagaccgtgtcgcctcaatcgacgcgtgaggacacgttgattcttatacggcgtctcag
+f10v7s84	f10v7s84	1.000000	T	224921	gtgccggacactcgcaatcttcacaagcagaggtccagctaacacacagcagcatttagtcccgatgggtagc
+f10v0s77	f10v0s77	1.000000	T	97674	ttgccggacactcgcaatcttccaagcagaggtccagctaacacacagcaggcatttagtcccgatgggtagc
+f5v6s59	f2v8s26	0.985075	F	619902	ggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v10s28	f2v8s26	0.985075	F	619902	ggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f1v5s14	f1v5s14	1.000000	T	95466	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f0v4s4	f1v5s14	1.000000	F	95466	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f0v1s1	f1v5s14	1.000000	F	95466	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f0v3s3	f1v5s14	1.000000	F	95466	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f5v3s56	f5v3s56	1.000000	T	142796	ccgcaacgcaccataagatgtaatcactaagaaaaatcggcctaacctgtcatatcgccactt
+f10v2s79	f10v2s79	1.000000	T	93964	ttgccggtcactcgcaatcttaccaaccagaggtccagctaacacacagcaggcatttagtcccgatgggtagc
+f10v13s90	f10v13s90	1.000000	T	92493	tgccggacactcgcaatctccaagcagagagtccaagctaacacacagcaggcatttgtcccgatgggtagc
+f1v4s13	f1v4s13	1.000000	T	93209	gaatcagcttctcaaccaagcgatgcagaaccggctactttaagcattgatgaatgcgtcgtaagtgatactggacgattc
+f10v4s81	f10v4s81	1.000000	T	88973	ttgccggacactggcaatcttccatagcagaggtccagctaacacacagcaggcatttagtcccgatgggtagc
+f10v5s82	f10v5s82	1.000000	T	87843	ttgccggacactcgcaatcttccaagcagaggtccagctaacacatagcaggcatttagtcccgatgggtagc
+f4v8s52	f4v8s52	1.000000	T	160201	ctgatattcgtattgatctactacgtatcaaagtatcccacttttgtgaccccactaagagaaga
+f2v11s29	f2v8s26	0.955882	F	619902	tggactgtagaaccgtgtgcctcaatccacgcgtgaggacacgttgatttcttatacggcgtctcag
+f0v6s6	f0v6s6	1.000000	T	84418	ggatcacagtctacactgctccctccaaccccggcccctggtccgaggagagggtgcttcagagtattataccactg
+f1v3s12	f0v6s6	1.000000	F	84418	ggatcacagtctacactgctccctccaaccccggcccctggtccgaggagagggtgcttcagagtattataccactg
+f0v0s0	f0v7s7	0.916667	F	281628	ggatcacagtctacactgctcactccaaccccggcccctgagtccgaggagagggtgcttcagagtatgtataccactg
+f0v2s2	f0v7s7	0.916667	F	281628	ggatcacagtctacactgctcactccaaccccggcccctgagtccgaggagagggtgcttcagagtatgtataccactg
+f1v7s16	f1v7s16	1.000000	T	81657	gaatcagcttcaaccaagcgatgcagaaccgctgctttaagcatgatgaatcgtcgtaagtgatactcgacgattc
+f2v5s23	f1v7s16	1.000000	F	81657	gaatcagcttcaaccaagcgatgcagaaccgctgctttaagcatgatgaatcgtcgtaagtgatactcgacgattc
+f3v12s43	f3v3s34	0.948718	F	670881	cgaaaaaggtgaatgaaagactgggacgcctcctggtttgggacgctctaggtggttgtggcttgaacgttagcacct
+f8v0s68	f8v0s68	1.000000	T	114020	aagaccttgaacacctctaagcgaaaattggattcgagtcagggaacataaccacgggtgcgt
+f2v1s19	f2v1s19	1.000000	T	79492	gaatcaggttcttccaagcgctgcagaaccggctactttaagcattgatgaatgcgtcagtaagtgatacccgacgattc
+f1v8s17	f2v1s19	1.000000	F	79492	gaatcaggttcttccaagcgctgcagaaccggctactttaagcattgatgaatgcgtcagtaagtgatacccgacgattc
+f10v11s88	f10v11s88	1.000000	T	78894	ttgccggacactcgcaatcttccaagcagaggtccagctaactcacagccaggcatttagtcccgatgggtagc
+f3v5s36	f3v3s34	0.973684	F	670881	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttatggcttgaaagttagcacct
+f8v7s75	f8v7s75	1.000000	T	75803	aagaccttgaacacctctaagcgaaaattggattccagtcagggaaccataaccacgggtgcgt
+f10v12s89	f10v12s89	1.000000	T	74438	ttgccggacactcgcaatcttccaagcagaggtccagctaacacacacgcaggcatttagacccgatgggtagc
+f4v2s46	f4v2s46	1.000000	T	83032	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagagaaga
+f8v2s70	f8v2s70	1.000000	T	74088	aagaccttgaacaacctctaagccgaaattggaattcgagtcagggaacataaccacgggtgcgat
+f11v8s99	f11v8s99	1.000000	T	224582	agcgttagcaaagagcctggttaatctgccctcgaggatcggtggtgatcagagatgcgggcatccgtttc
+f7v0s64	f7v0s64	1.000000	T	114016	gcttcgtgggaaccagagacaaccgacatatttcgaaccaccgacatacgatccttaaacc
+f11v1s92	f11v1s92	1.000000	T	71853	agcgttagcaaagagcctggttcatcgccctcgaggatcggtggtgatcaagagatgcggcatccgtttc
+f3v2s33	f3v3s34	0.948052	F	670881	cgaaaaaaggtaatgaaaggctgggatgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcact
+f8v3s71	f8v3s71	1.000000	T	70497	aagaccttgaacacctctaagcgaaattggattcgagtcagcgaacataacacgggtgcgt
+f4v3s47	f4v3s47	1.000000	T	69396	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaaagaaga
+f10v10s87	f10v10s87	1.000000	T	66794	tctgccggacactcgcaatcttccaagcagaggtccagctaacacacgcaggcatttatccgatgggtagc
+f11v0s91	f11v0s91	1.000000	T	66160	agcgttagcaaagagcctggttaatcgccctcgaggatcggtggtgatcagagatgcgggcatccgtttc
+f8v5s73	f8v5s73	1.000000	T	64084	aagaccttgtacacctctaagcgataaattggattcgagtcagggaacataaccacggatgcgt
+f8v4s72	f8v4s72	1.000000	T	59724	aagacttgaacacctctaagcgaaaattggattcgagtcagggaacataaccacgggtgcgt
+f3v1s32	f3v3s34	0.974359	F	670881	cgaaaaagagtgaatgaaatggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f3v4s35	f3v3s34	0.948052	F	670881	cgaaaaaggtgaagaaaggctgggacgctcctggttggcgcgctctaggtgttgtggcttgaacgttagcaccta
+f11v6s97	f11v6s97	1.000000	T	58908	agcgttagcaaagaacctggttaatcgccctcgaggatcggtggtggatcggagatgcgggcatcgcgtttc
+f4v1s45	f4v1s45	1.000000	T	55908	ctgtatttcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactatagagaaga
+f0v5s5	f0v5s5	1.000000	T	54120	ggatcacagtctacactgctcactcccccccggcccctgagtccgaggagagggtgcttcaaagtatgtataccactg
+f5v5s58	f5v5s58	1.000000	T	49852	cgcaacgcaccattaagatggtaatcactaaaaaaatcggcctaacctgtccaatcgccactt
+f1v0s9	f1v0s9	1.000000	T	49791	gaatcagcttctaaccaagcgatgcagaaccggctactttaagcattgatgaatgcgtcgtaagtgatactcgacgattc
+f8v6s74	f8v6s74	1.000000	T	49062	aagacccttgaacacctctaagcgaaaattggattcgagtcagggaacataaccacgggtgccgt
+f6v0s60	f6v0s60	1.000000	T	67982	catgtcaagagactggaaccccggtgatgtgaaaaaaggtcttgggtacgtcccatggctacg
+f10v8s85	f10v7s84	0.920000	F	224921	ttgccggacactcgaatcttccaagcagaggtccagctaacacacagcaggcatactagtcccgatgggtagc
+f10v1s78	f10v7s84	0.933333	F	224921	ttgccggacactcgcaatcctccaagcagaggtccagctaacacacagcaggcatttagtcccgatgaggtagc
+f5v4s57	f5v3s56	0.924242	F	142796	cggcaacgcaccataagatggtaatcactaaaaaaatcggcctaacctgtccatatcgccactat
+f3v10s41	f3v3s34	0.948718	F	670881	cgaaaataaggtgaatgaaagggtgggacgctcctagtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f3v7s38	f3v3s34	0.974026	F	670881	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttcgtgcttgaacgttagcacct
+f10v6s83	f10v7s84	0.932432	F	224921	ttccggacactcgcaatcttccaagcagaggtccagctaacacacagcaggcatttagtcctgatgggtagc
+f11v2s93	f11v8s99	0.958333	F	224582	agcgttagcaaagagcctggttaatcgccctcggaggatcggtggtgatcagagatgcgggcatccgttc
+f3v9s40	f3v3s34	0.986842	F	670881	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggggttgtggcttgaacgttagcacct
+f11v4s95	f11v8s99	0.944444	F	224582	agcgttagcaaagagcctggttaatcccctcgagatcgggtggtgatcagagatgcgggcatccgtttc
+f8v1s69	f8v0s68	0.984375	F	114020	aagaccttgaacacctctaagcgaaaattggatatcgagtcagggaacataaccacgggtgcgt
+f11v5s96	f11v8s99	0.944444	F	224582	agcgttagcaaagagcctggttaatggccctcgaggatcggtggctgaccagagatgcgggcatccgtttc
+f6v2s62	f6v2s62	1.000000	T	33001	catgtcgagagactggaaccccggtgatgtgaaaaaaggtcttgggtacgtcccatggctac
+f4v6s50	f4v8s52	0.910448	F	160201	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagacgaagag
+f9v0s76	f9v0s76	1.000000	T	29993	gggatcgtggcaagcaacccttgccgcctcgactgcggctaaagacgcatgttccagtaataccta
+f2v12s30	f2v8s26	0.955224	F	619902	tggactagtagaccgtgtgccacaatcgacgctgaggacacgttgatttttatacggcgtctcag
+f11v9s100	f11v8s99	0.972222	F	224582	agcgttagcaaaggagcctggttaatcgccctcgaggatcggtggtgatcagagatgcgggcatccgtttc
+f4v5s49	f4v8s52	0.924242	F	160201	ctatattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagagaagca
+f2v9s27	f2v8s26	0.985075	F	619902	tggactagtagaccgtgtgcctaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f7v3s67	f7v0s64	0.983607	F	114016	gcttcgtgggaccagagacaaccgacatatttcgaaccaccgacatacgatccttaaacc
+f0v8s8	f0v7s7	0.905882	F	281628	ggatcacagtcctacactgctcactccaaccccggccctgagtccgaggagagggtgcttcagagtatgtataccactg
+f2v6s24	f2v8s26	0.940299	F	619902	tggactagtagacgtgtgcctcatcgacgcgtgagacactttgatttcttatacggcgtctcag
+f11v3s94	f11v8s99	0.958333	F	224582	agcgttagcaaagagcctggttaatcgccgtcgaaggatcggtggtgatcagagatgcgggcatccgtttc
+f6v3s63	f6v0s60	0.953846	F	67982	catgtcaagagactggaaccccggtgatgtgaaaaaaggttttgggtcacgtctccatggctacg
+f3v11s42	f3v3s34	0.973684	F	670881	cgaaaaaggtgaatgaaagtctgggacgctcctggtttgggacgctctaggtgttgtggcttgaacgttagcacct
+f4v4s48	f4v8s52	0.923077	F	160201	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagagaaa
+f3v8s39	f3v3s34	0.948052	F	670881	cgaaaaaggtgaatgaaaggcctgggacgctcctggttggggcgctctaggtgtgtggcttgaacgttagacct
+f7v1s65	f7v0s64	0.967742	F	114016	gcttcggggaaccagagacaaccgacatatttcgaaccaccgacatacgatcctttaaacc
+f5v1s54	f5v3s56	0.923077	F	142796	cggaacgcaccataagatggtaatcactaaaaaaatcggcctaacctgtccatatcgccactt
+f4v7s51	f4v2s46	0.937500	F	83032	cgtttattcgtaggatctactacgcatcaaagtatcccacttttgtaccccactaagagcaga
+f7v2s66	f7v0s64	0.951613	F	114016	gcttcgtgggaaccagaacaaccgacatattccgaaccaccggacatacgatccttaaacc
+f1v6s15	f1v4s13	0.950617	F	93209	gaatcagcttctaaccaagcgttgcagaaccggctactttaagcatgatgaatgcgtcgtaagtgatactcgacgattc
+f5v2s55	f5v3s56	0.907692	F	142796	cggcatcgcaccataagatggtaatcactaaaaaaatcggcctaacctgtccatatcgccact

pkg/obitools/obiclust/testdata/families_rawdist.expected

@@ -0,0 +1,101 @@
+f2v8s26	f2v8s26	0.000000	T	863655	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f10v3s80	f2v8s26	0.000000	F	863655	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v0s18	f2v8s26	0.000000	F	863655	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v7s25	f2v8s26	0.000000	F	863655	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f10v9s86	f2v8s26	0.000000	F	863655	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v3s21	f2v8s26	1.000000	F	863655	tggactagtagaccgtgtgcctcaatcgacgcggaggacacgttgatttcttatacggcgtctcag
+f6v1s61	f2v8s26	1.000000	F	863655	tggactagtagaccgtgtgcctcaatcgacgcggaggacacgttgatttcttatacggcgtctcag
+f2v2s20	f2v8s26	1.000000	F	863655	tggactagtagaccgtgtgcctcaatcgacgcggaggacacgttgatttcttatacggcgtctcag
+f3v3s34	f3v3s34	0.000000	T	670881	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f4v0s44	f3v3s34	0.000000	F	670881	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f3v0s31	f3v3s34	0.000000	F	670881	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f0v7s7	f0v7s7	0.000000	T	173457	ggatcacacgtctatcactgctcactccaaccccggcccttgacgtccgaggagagggtgcttctgagtatgtatacccaactg
+f1v2s11	f0v7s7	0.000000	F	173457	ggatcacacgtctatcactgctcactccaaccccggcccttgacgtccgaggagagggtgcttctgagtatgtatacccaactg
+f1v1s10	f0v7s7	0.000000	F	173457	ggatcacacgtctatcactgctcactccaaccccggcccttgacgtccgaggagagggtgcttctgagtatgtatacccaactg
+f3v6s37	f3v6s37	0.000000	T	167833	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgtctctaggttgttgtggctgaacgtagcact
+f5v0s53	f3v6s37	0.000000	F	167833	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgtctctaggttgttgtggctgaacgtagcact
+f11v7s98	f3v6s37	0.000000	F	167833	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgtctctaggttgttgtggctgaacgtagcact
+f2v4s22	f2v8s26	2.000000	F	863655	tggactagtagaccgtgtcgcctcaatcgacgcgtgaggacacgttgattcttatacggcgtctcag
+f10v7s84	f10v7s84	0.000000	T	196352	gtgccggacactcgcaatcttcacaagcagaggtccagctaacacacagcagcatttagtcccgatgggtagc
+f10v0s77	f10v7s84	3.000000	F	196352	ttgccggacactcgcaatcttccaagcagaggtccagctaacacacagcaggcatttagtcccgatgggtagc
+f5v6s59	f2v8s26	1.000000	F	863655	ggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v10s28	f2v8s26	1.000000	F	863655	ggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f1v5s14	f1v5s14	0.000000	T	203637	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f0v4s4	f1v5s14	0.000000	F	203637	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f0v1s1	f1v5s14	0.000000	F	203637	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f0v3s3	f1v5s14	0.000000	F	203637	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f5v3s56	f5v3s56	0.000000	T	94426	ccgcaacgcaccataagatgtaatcactaagaaaaatcggcctaacctgtcatatcgccactt
+f10v2s79	f10v2s79	0.000000	T	93964	ttgccggtcactcgcaatcttaccaaccagaggtccagctaacacacagcaggcatttagtcccgatgggtagc
+f10v13s90	f10v13s90	0.000000	T	92493	tgccggacactcgcaatctccaagcagagagtccaagctaacacacagcaggcatttgtcccgatgggtagc
+f1v4s13	f1v4s13	0.000000	T	143000	gaatcagcttctcaaccaagcgatgcagaaccggctactttaagcattgatgaatgcgtcgtaagtgatactggacgattc
+f10v4s81	f10v4s81	0.000000	T	409687	ttgccggacactggcaatcttccatagcagaggtccagctaacacacagcaggcatttagtcccgatgggtagc
+f10v5s82	f10v4s81	3.000000	F	409687	ttgccggacactcgcaatcttccaagcagaggtccagctaacacatagcaggcatttagtcccgatgggtagc
+f4v8s52	f4v8s52	0.000000	T	161072	ctgatattcgtattgatctactacgtatcaaagtatcccacttttgtgaccccactaagagaaga
+f2v11s29	f2v8s26	3.000000	F	863655	tggactgtagaaccgtgtgcctcaatccacgcgtgaggacacgttgatttcttatacggcgtctcag
+f0v6s6	f0v6s6	0.000000	T	84418	ggatcacagtctacactgctccctccaaccccggcccctggtccgaggagagggtgcttcagagtattataccactg
+f1v3s12	f0v6s6	0.000000	F	84418	ggatcacagtctacactgctccctccaaccccggcccctggtccgaggagagggtgcttcagagtattataccactg
+f0v0s0	f1v5s14	3.000000	F	203637	ggatcacagtctacactgctcactccaaccccggcccctgagtccgaggagagggtgcttcagagtatgtataccactg
+f0v2s2	f1v5s14	3.000000	F	203637	ggatcacagtctacactgctcactccaaccccggcccctgagtccgaggagagggtgcttcagagtatgtataccactg
+f1v7s16	f1v7s16	0.000000	T	81657	gaatcagcttcaaccaagcgatgcagaaccgctgctttaagcatgatgaatcgtcgtaagtgatactcgacgattc
+f2v5s23	f1v7s16	0.000000	F	81657	gaatcagcttcaaccaagcgatgcagaaccgctgctttaagcatgatgaatcgtcgtaagtgatactcgacgattc
+f3v12s43	f3v3s34	4.000000	F	670881	cgaaaaaggtgaatgaaagactgggacgcctcctggtttgggacgctctaggtggttgtggcttgaacgttagcacct
+f8v0s68	f8v0s68	0.000000	T	433190	aagaccttgaacacctctaagcgaaaattggattcgagtcagggaacataaccacgggtgcgt
+f2v1s19	f2v1s19	0.000000	T	79492	gaatcaggttcttccaagcgctgcagaaccggctactttaagcattgatgaatgcgtcagtaagtgatacccgacgattc
+f1v8s17	f2v1s19	0.000000	F	79492	gaatcaggttcttccaagcgctgcagaaccggctactttaagcattgatgaatgcgtcagtaagtgatacccgacgattc
+f10v11s88	f10v4s81	4.000000	F	409687	ttgccggacactcgcaatcttccaagcagaggtccagctaactcacagccaggcatttagtcccgatgggtagc
+f3v5s36	f3v3s34	2.000000	F	670881	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttatggcttgaaagttagcacct
+f8v7s75	f8v0s68	2.000000	F	433190	aagaccttgaacacctctaagcgaaaattggattccagtcagggaaccataaccacgggtgcgt
+f10v12s89	f10v4s81	4.000000	F	409687	ttgccggacactcgcaatcttccaagcagaggtccagctaacacacacgcaggcatttagacccgatgggtagc
+f4v2s46	f4v8s52	4.000000	F	161072	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagagaaga
+f8v2s70	f8v2s70	0.000000	T	74088	aagaccttgaacaacctctaagccgaaattggaattcgagtcagggaacataaccacgggtgcgat
+f11v8s99	f11v8s99	0.000000	T	362595	agcgttagcaaagagcctggttaatctgccctcgaggatcggtggtgatcagagatgcgggcatccgtttc
+f7v0s64	f7v0s64	0.000000	T	114016	gcttcgtgggaaccagagacaaccgacatatttcgaaccaccgacatacgatccttaaacc
+f11v1s92	f11v8s99	4.000000	F	362595	agcgttagcaaagagcctggttcatcgccctcgaggatcggtggtgatcaagagatgcggcatccgtttc
+f3v2s33	f3v3s34	4.000000	F	670881	cgaaaaaaggtaatgaaaggctgggatgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcact
+f8v3s71	f8v0s68	3.000000	F	433190	aagaccttgaacacctctaagcgaaattggattcgagtcagcgaacataacacgggtgcgt
+f4v3s47	f4v3s47	0.000000	T	198866	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaaagaaga
+f10v10s87	f10v10s87	0.000000	T	66794	tctgccggacactcgcaatcttccaagcagaggtccagctaacacacgcaggcatttatccgatgggtagc
+f11v0s91	f11v8s99	1.000000	F	362595	agcgttagcaaagagcctggttaatcgccctcgaggatcggtggtgatcagagatgcgggcatccgtttc
+f8v5s73	f8v0s68	3.000000	F	433190	aagaccttgtacacctctaagcgataaattggattcgagtcagggaacataaccacggatgcgt
+f8v4s72	f8v0s68	1.000000	F	433190	aagacttgaacacctctaagcgaaaattggattcgagtcagggaacataaccacgggtgcgt
+f3v1s32	f3v3s34	2.000000	F	670881	cgaaaaagagtgaatgaaatggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f3v4s35	f3v3s34	4.000000	F	670881	cgaaaaaggtgaagaaaggctgggacgctcctggttggcgcgctctaggtgttgtggcttgaacgttagcaccta
+f11v6s97	f11v6s97	0.000000	T	58908	agcgttagcaaagaacctggttaatcgccctcgaggatcggtggtggatcggagatgcgggcatcgcgtttc
+f4v1s45	f4v3s47	3.000000	F	198866	ctgtatttcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactatagagaaga
+f0v5s5	f0v5s5	0.000000	T	54120	ggatcacagtctacactgctcactcccccccggcccctgagtccgaggagagggtgcttcaaagtatgtataccactg
+f5v5s58	f5v5s58	0.000000	T	97556	cgcaacgcaccattaagatggtaatcactaaaaaaatcggcctaacctgtccaatcgccactt
+f1v0s9	f1v4s13	2.000000	F	143000	gaatcagcttctaaccaagcgatgcagaaccggctactttaagcattgatgaatgcgtcgtaagtgatactcgacgattc
+f8v6s74	f8v0s68	2.000000	F	433190	aagacccttgaacacctctaagcgaaaattggattcgagtcagggaacataaccacgggtgccgt
+f6v0s60	f6v0s60	0.000000	T	100983	catgtcaagagactggaaccccggtgatgtgaaaaaaggtcttgggtacgtcccatggctacg
+f10v8s85	f10v8s85	0.000000	T	46704	ttgccggacactcgaatcttccaagcagaggtccagctaacacacagcaggcatactagtcccgatgggtagc
+f10v1s78	f10v4s81	4.000000	F	409687	ttgccggacactcgcaatcctccaagcagaggtccagctaacacacagcaggcatttagtcccgatgaggtagc
+f5v4s57	f5v5s58	4.000000	F	97556	cggcaacgcaccataagatggtaatcactaaaaaaatcggcctaacctgtccatatcgccactat
+f3v10s41	f3v3s34	4.000000	F	670881	cgaaaataaggtgaatgaaagggtgggacgctcctagtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f3v7s38	f3v3s34	2.000000	F	670881	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttcgtgcttgaacgttagcacct
+f10v6s83	f10v4s81	4.000000	F	409687	ttccggacactcgcaatcttccaagcagaggtccagctaacacacagcaggcatttagtcctgatgggtagc
+f11v2s93	f11v8s99	3.000000	F	362595	agcgttagcaaagagcctggttaatcgccctcggaggatcggtggtgatcagagatgcgggcatccgttc
+f3v9s40	f3v3s34	1.000000	F	670881	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggggttgtggcttgaacgttagcacct
+f11v4s95	f11v8s99	4.000000	F	362595	agcgttagcaaagagcctggttaatcccctcgagatcgggtggtgatcagagatgcgggcatccgtttc
+f8v1s69	f8v0s68	1.000000	F	433190	aagaccttgaacacctctaagcgaaaattggatatcgagtcagggaacataaccacgggtgcgt
+f11v5s96	f11v8s99	4.000000	F	362595	agcgttagcaaagagcctggttaatggccctcgaggatcggtggctgaccagagatgcgggcatccgtttc
+f6v2s62	f6v0s60	2.000000	F	100983	catgtcgagagactggaaccccggtgatgtgaaaaaaggtcttgggtacgtcccatggctac
+f4v6s50	f4v3s47	3.000000	F	198866	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagacgaagag
+f9v0s76	f9v0s76	0.000000	T	29993	gggatcgtggcaagcaacccttgccgcctcgactgcggctaaagacgcatgttccagtaataccta
+f2v12s30	f2v8s26	3.000000	F	863655	tggactagtagaccgtgtgccacaatcgacgctgaggacacgttgatttttatacggcgtctcag
+f11v9s100	f11v8s99	2.000000	F	362595	agcgttagcaaaggagcctggttaatcgccctcgaggatcggtggtgatcagagatgcgggcatccgtttc
+f4v5s49	f4v3s47	3.000000	F	198866	ctatattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagagaagca
+f2v9s27	f2v8s26	1.000000	F	863655	tggactagtagaccgtgtgcctaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f7v3s67	f7v0s64	1.000000	F	114016	gcttcgtgggaccagagacaaccgacatatttcgaaccaccgacatacgatccttaaacc
+f0v8s8	f1v5s14	4.000000	F	203637	ggatcacagtcctacactgctcactccaaccccggccctgagtccgaggagagggtgcttcagagtatgtataccactg
+f2v6s24	f2v8s26	4.000000	F	863655	tggactagtagacgtgtgcctcatcgacgcgtgagacactttgatttcttatacggcgtctcag
+f11v3s94	f11v8s99	3.000000	F	362595	agcgttagcaaagagcctggttaatcgccgtcgaaggatcggtggtgatcagagatgcgggcatccgtttc
+f6v3s63	f6v0s60	3.000000	F	100983	catgtcaagagactggaaccccggtgatgtgaaaaaaggttttgggtcacgtctccatggctacg
+f3v11s42	f3v3s34	2.000000	F	670881	cgaaaaaggtgaatgaaagtctgggacgctcctggtttgggacgctctaggtgttgtggcttgaacgttagcacct
+f4v4s48	f4v3s47	2.000000	F	198866	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagagaaa
+f3v8s39	f3v3s34	4.000000	F	670881	cgaaaaaggtgaatgaaaggcctgggacgctcctggttggggcgctctaggtgtgtggcttgaacgttagacct
+f7v1s65	f7v0s64	2.000000	F	114016	gcttcggggaaccagagacaaccgacatatttcgaaccaccgacatacgatcctttaaacc
+f5v1s54	f5v5s58	3.000000	F	97556	cggaacgcaccataagatggtaatcactaaaaaaatcggcctaacctgtccatatcgccactt
+f4v7s51	f4v7s51	0.000000	T	8599	cgtttattcgtaggatctactacgcatcaaagtatcccacttttgtaccccactaagagcaga
+f7v2s66	f7v0s64	3.000000	F	114016	gcttcgtgggaaccagaacaaccgacatattccgaaccaccggacatacgatccttaaacc
+f1v6s15	f1v4s13	4.000000	F	143000	gaatcagcttctaaccaagcgttgcagaaccggctactttaagcatgatgaatgcgtcgtaagtgatactcgacgattc
+f5v2s55	f5v2s55	0.000000	T	666	cggcatcgcaccataagatggtaatcactaaaaaaatcggcctaacctgtccatatcgccact

pkg/obitools/obiclust/testdata/families_rawlcs.expected

@@ -0,0 +1,101 @@
+f2v8s26	f2v8s26	67.000000	T	4505217	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f10v3s80	f2v8s26	67.000000	F	4505217	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v0s18	f2v8s26	67.000000	F	4505217	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v7s25	f2v8s26	67.000000	F	4505217	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f10v9s86	f2v8s26	67.000000	F	4505217	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v3s21	f2v8s26	66.000000	F	4505217	tggactagtagaccgtgtgcctcaatcgacgcggaggacacgttgatttcttatacggcgtctcag
+f6v1s61	f2v8s26	66.000000	F	4505217	tggactagtagaccgtgtgcctcaatcgacgcggaggacacgttgatttcttatacggcgtctcag
+f2v2s20	f2v8s26	66.000000	F	4505217	tggactagtagaccgtgtgcctcaatcgacgcggaggacacgttgatttcttatacggcgtctcag
+f3v3s34	f2v8s26	42.000000	F	4505217	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f4v0s44	f2v8s26	42.000000	F	4505217	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f3v0s31	f2v8s26	42.000000	F	4505217	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f0v7s7	f2v8s26	48.000000	F	4505217	ggatcacacgtctatcactgctcactccaaccccggcccttgacgtccgaggagagggtgcttctgagtatgtatacccaactg
+f1v2s11	f2v8s26	48.000000	F	4505217	ggatcacacgtctatcactgctcactccaaccccggcccttgacgtccgaggagagggtgcttctgagtatgtatacccaactg
+f1v1s10	f2v8s26	48.000000	F	4505217	ggatcacacgtctatcactgctcactccaaccccggcccttgacgtccgaggagagggtgcttctgagtatgtatacccaactg
+f3v6s37	f2v8s26	43.000000	F	4505217	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgtctctaggttgttgtggctgaacgtagcact
+f5v0s53	f2v8s26	43.000000	F	4505217	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgtctctaggttgttgtggctgaacgtagcact
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+f2v4s22	f2v8s26	66.000000	F	4505217	tggactagtagaccgtgtcgcctcaatcgacgcgtgaggacacgttgattcttatacggcgtctcag
+f10v7s84	f2v8s26	43.000000	F	4505217	gtgccggacactcgcaatcttcacaagcagaggtccagctaacacacagcagcatttagtcccgatgggtagc
+f10v0s77	f2v8s26	43.000000	F	4505217	ttgccggacactcgcaatcttccaagcagaggtccagctaacacacagcaggcatttagtcccgatgggtagc
+f5v6s59	f2v8s26	66.000000	F	4505217	ggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v10s28	f2v8s26	66.000000	F	4505217	ggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f1v5s14	f2v8s26	46.000000	F	4505217	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f0v4s4	f2v8s26	46.000000	F	4505217	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f0v1s1	f2v8s26	46.000000	F	4505217	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f0v3s3	f2v8s26	46.000000	F	4505217	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f5v3s56	f5v3s56	63.000000	T	229172	ccgcaacgcaccataagatgtaatcactaagaaaaatcggcctaacctgtcatatcgccactt
+f10v2s79	f2v8s26	43.000000	F	4505217	ttgccggtcactcgcaatcttaccaaccagaggtccagctaacacacagcaggcatttagtcccgatgggtagc
+f10v13s90	f2v8s26	43.000000	F	4505217	tgccggacactcgcaatctccaagcagagagtccaagctaacacacagcaggcatttgtcccgatgggtagc
+f1v4s13	f2v8s26	49.000000	F	4505217	gaatcagcttctcaaccaagcgatgcagaaccggctactttaagcattgatgaatgcgtcgtaagtgatactggacgattc
+f10v4s81	f2v8s26	44.000000	F	4505217	ttgccggacactggcaatcttccatagcagaggtccagctaacacacagcaggcatttagtcccgatgggtagc
+f10v5s82	f2v8s26	43.000000	F	4505217	ttgccggacactcgcaatcttccaagcagaggtccagctaacacatagcaggcatttagtcccgatgggtagc
+f4v8s52	f4v8s52	65.000000	T	254973	ctgatattcgtattgatctactacgtatcaaagtatcccacttttgtgaccccactaagagaaga
+f2v11s29	f2v8s26	65.000000	F	4505217	tggactgtagaaccgtgtgcctcaatccacgcgtgaggacacgttgatttcttatacggcgtctcag
+f0v6s6	f2v8s26	47.000000	F	4505217	ggatcacagtctacactgctccctccaaccccggcccctggtccgaggagagggtgcttcagagtattataccactg
+f1v3s12	f2v8s26	47.000000	F	4505217	ggatcacagtctacactgctccctccaaccccggcccctggtccgaggagagggtgcttcagagtattataccactg
+f0v0s0	f2v8s26	47.000000	F	4505217	ggatcacagtctacactgctcactccaaccccggcccctgagtccgaggagagggtgcttcagagtatgtataccactg
+f0v2s2	f2v8s26	47.000000	F	4505217	ggatcacagtctacactgctcactccaaccccggcccctgagtccgaggagagggtgcttcagagtatgtataccactg
+f1v7s16	f2v8s26	46.000000	F	4505217	gaatcagcttcaaccaagcgatgcagaaccgctgctttaagcatgatgaatcgtcgtaagtgatactcgacgattc
+f2v5s23	f2v8s26	46.000000	F	4505217	gaatcagcttcaaccaagcgatgcagaaccgctgctttaagcatgatgaatcgtcgtaagtgatactcgacgattc
+f3v12s43	f2v8s26	44.000000	F	4505217	cgaaaaaggtgaatgaaagactgggacgcctcctggtttgggacgctctaggtggttgtggcttgaacgttagcacct
+f8v0s68	f2v8s26	40.000000	F	4505217	aagaccttgaacacctctaagcgaaaattggattcgagtcagggaacataaccacgggtgcgt
+f2v1s19	f2v8s26	47.000000	F	4505217	gaatcaggttcttccaagcgctgcagaaccggctactttaagcattgatgaatgcgtcagtaagtgatacccgacgattc
+f1v8s17	f2v8s26	47.000000	F	4505217	gaatcaggttcttccaagcgctgcagaaccggctactttaagcattgatgaatgcgtcagtaagtgatacccgacgattc
+f10v11s88	f2v8s26	43.000000	F	4505217	ttgccggacactcgcaatcttccaagcagaggtccagctaactcacagccaggcatttagtcccgatgggtagc
+f3v5s36	f2v8s26	43.000000	F	4505217	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttatggcttgaaagttagcacct
+f8v7s75	f5v3s56	41.000000	F	229172	aagaccttgaacacctctaagcgaaaattggattccagtcagggaaccataaccacgggtgcgt
+f10v12s89	f2v8s26	43.000000	F	4505217	ttgccggacactcgcaatcttccaagcagaggtccagctaacacacacgcaggcatttagacccgatgggtagc
+f4v2s46	f4v8s52	61.000000	F	254973	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagagaaga
+f8v2s70	f2v8s26	40.000000	F	4505217	aagaccttgaacaacctctaagccgaaattggaattcgagtcagggaacataaccacgggtgcgat
+f11v8s99	f2v8s26	45.000000	F	4505217	agcgttagcaaagagcctggttaatctgccctcgaggatcggtggtgatcagagatgcgggcatccgtttc
+f7v0s64	f7v0s64	61.000000	T	114016	gcttcgtgggaaccagagacaaccgacatatttcgaaccaccgacatacgatccttaaacc
+f11v1s92	f2v8s26	45.000000	F	4505217	agcgttagcaaagagcctggttcatcgccctcgaggatcggtggtgatcaagagatgcggcatccgtttc
+f3v2s33	f2v8s26	42.000000	F	4505217	cgaaaaaaggtaatgaaaggctgggatgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcact
+f8v3s71	f2v8s26	40.000000	F	4505217	aagaccttgaacacctctaagcgaaattggattcgagtcagcgaacataacacgggtgcgt
+f4v3s47	f4v8s52	60.000000	F	254973	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaaagaaga
+f10v10s87	f2v8s26	43.000000	F	4505217	tctgccggacactcgcaatcttccaagcagaggtccagctaacacacgcaggcatttatccgatgggtagc
+f11v0s91	f2v8s26	45.000000	F	4505217	agcgttagcaaagagcctggttaatcgccctcgaggatcggtggtgatcagagatgcgggcatccgtttc
+f8v5s73	f2v8s26	40.000000	F	4505217	aagaccttgtacacctctaagcgataaattggattcgagtcagggaacataaccacggatgcgt
+f8v4s72	f8v4s72	62.000000	T	59724	aagacttgaacacctctaagcgaaaattggattcgagtcagggaacataaccacgggtgcgt
+f3v1s32	f2v8s26	44.000000	F	4505217	cgaaaaagagtgaatgaaatggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f3v4s35	f2v8s26	43.000000	F	4505217	cgaaaaaggtgaagaaaggctgggacgctcctggttggcgcgctctaggtgttgtggcttgaacgttagcaccta
+f11v6s97	f2v8s26	45.000000	F	4505217	agcgttagcaaagaacctggttaatcgccctcgaggatcggtggtggatcggagatgcgggcatcgcgtttc
+f4v1s45	f2v8s26	40.000000	F	4505217	ctgtatttcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactatagagaaga
+f0v5s5	f2v8s26	45.000000	F	4505217	ggatcacagtctacactgctcactcccccccggcccctgagtccgaggagagggtgcttcaaagtatgtataccactg
+f5v5s58	f5v3s56	60.000000	F	229172	cgcaacgcaccattaagatggtaatcactaaaaaaatcggcctaacctgtccaatcgccactt
+f1v0s9	f2v8s26	47.000000	F	4505217	gaatcagcttctaaccaagcgatgcagaaccggctactttaagcattgatgaatgcgtcgtaagtgatactcgacgattc
+f8v6s74	f2v8s26	41.000000	F	4505217	aagacccttgaacacctctaagcgaaaattggattcgagtcagggaacataaccacgggtgccgt
+f6v0s60	f2v8s26	41.000000	F	4505217	catgtcaagagactggaaccccggtgatgtgaaaaaaggtcttgggtacgtcccatggctacg
+f10v8s85	f2v8s26	43.000000	F	4505217	ttgccggacactcgaatcttccaagcagaggtccagctaacacacagcaggcatactagtcccgatgggtagc
+f10v1s78	f2v8s26	44.000000	F	4505217	ttgccggacactcgcaatcctccaagcagaggtccagctaacacacagcaggcatttagtcccgatgaggtagc
+f5v4s57	f2v8s26	41.000000	F	4505217	cggcaacgcaccataagatggtaatcactaaaaaaatcggcctaacctgtccatatcgccactat
+f3v10s41	f2v8s26	43.000000	F	4505217	cgaaaataaggtgaatgaaagggtgggacgctcctagtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f3v7s38	f2v8s26	43.000000	F	4505217	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttcgtgcttgaacgttagcacct
+f10v6s83	f2v8s26	44.000000	F	4505217	ttccggacactcgcaatcttccaagcagaggtccagctaacacacagcaggcatttagtcctgatgggtagc
+f11v2s93	f2v8s26	45.000000	F	4505217	agcgttagcaaagagcctggttaatcgccctcggaggatcggtggtgatcagagatgcgggcatccgttc
+f3v9s40	f2v8s26	42.000000	F	4505217	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggggttgtggcttgaacgttagcacct
+f11v4s95	f2v8s26	44.000000	F	4505217	agcgttagcaaagagcctggttaatcccctcgagatcgggtggtgatcagagatgcgggcatccgtttc
+f8v1s69	f2v8s26	40.000000	F	4505217	aagaccttgaacacctctaagcgaaaattggatatcgagtcagggaacataaccacgggtgcgt
+f11v5s96	f2v8s26	44.000000	F	4505217	agcgttagcaaagagcctggttaatggccctcgaggatcggtggctgaccagagatgcgggcatccgtttc
+f6v2s62	f2v8s26	40.000000	F	4505217	catgtcgagagactggaaccccggtgatgtgaaaaaaggtcttgggtacgtcccatggctac
+f4v6s50	f2v8s26	40.000000	F	4505217	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagacgaagag
+f9v0s76	f2v8s26	44.000000	F	4505217	gggatcgtggcaagcaacccttgccgcctcgactgcggctaaagacgcatgttccagtaataccta
+f2v12s30	f2v8s26	64.000000	F	4505217	tggactagtagaccgtgtgccacaatcgacgctgaggacacgttgatttttatacggcgtctcag
+f11v9s100	f2v8s26	45.000000	F	4505217	agcgttagcaaaggagcctggttaatcgccctcgaggatcggtggtgatcagagatgcgggcatccgtttc
+f4v5s49	f2v8s26	40.000000	F	4505217	ctatattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagagaagca
+f2v9s27	f2v8s26	66.000000	F	4505217	tggactagtagaccgtgtgcctaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f7v3s67	f7v0s64	60.000000	F	114016	gcttcgtgggaccagagacaaccgacatatttcgaaccaccgacatacgatccttaaacc
+f0v8s8	f2v8s26	47.000000	F	4505217	ggatcacagtcctacactgctcactccaaccccggccctgagtccgaggagagggtgcttcagagtatgtataccactg
+f2v6s24	f2v8s26	63.000000	F	4505217	tggactagtagacgtgtgcctcatcgacgcgtgagacactttgatttcttatacggcgtctcag
+f11v3s94	f2v8s26	46.000000	F	4505217	agcgttagcaaagagcctggttaatcgccgtcgaaggatcggtggtgatcagagatgcgggcatccgtttc
+f6v3s63	f2v8s26	42.000000	F	4505217	catgtcaagagactggaaccccggtgatgtgaaaaaaggttttgggtcacgtctccatggctacg
+f3v11s42	f2v8s26	44.000000	F	4505217	cgaaaaaggtgaatgaaagtctgggacgctcctggtttgggacgctctaggtgttgtggcttgaacgttagcacct
+f4v4s48	f4v8s52	60.000000	F	254973	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagagaaa
+f3v8s39	f2v8s26	43.000000	F	4505217	cgaaaaaggtgaatgaaaggcctgggacgctcctggttggggcgctctaggtgtgtggcttgaacgttagacct
+f7v1s65	f7v0s64	60.000000	F	114016	gcttcggggaaccagagacaaccgacatatttcgaaccaccgacatacgatcctttaaacc
+f5v1s54	f5v3s56	60.000000	F	229172	cggaacgcaccataagatggtaatcactaaaaaaatcggcctaacctgtccatatcgccactt
+f4v7s51	f4v8s52	58.000000	F	254973	cgtttattcgtaggatctactacgcatcaaagtatcccacttttgtaccccactaagagcaga
+f7v2s66	f7v0s64	59.000000	F	114016	gcttcgtgggaaccagaacaaccgacatattccgaaccaccggacatacgatccttaaacc
+f1v6s15	f2v8s26	46.000000	F	4505217	gaatcagcttctaaccaagcgttgcagaaccggctactttaagcatgatgaatgcgtcgtaagtgatactcgacgattc
+f5v2s55	f2v8s26	40.000000	F	4505217	cggcatcgcaccataagatggtaatcactaaaaaaatcggcctaacctgtccatatcgccact

pkg/obitools/obiclust/testdata/families_shortest.expected

@@ -0,0 +1,101 @@
+f2v8s26	f2v8s26	1.000000	T	863655	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f10v3s80	f2v8s26	1.000000	F	863655	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v0s18	f2v8s26	1.000000	F	863655	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v7s25	f2v8s26	1.000000	F	863655	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f10v9s86	f2v8s26	1.000000	F	863655	tggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v3s21	f2v8s26	1.000000	F	863655	tggactagtagaccgtgtgcctcaatcgacgcggaggacacgttgatttcttatacggcgtctcag
+f6v1s61	f2v8s26	1.000000	F	863655	tggactagtagaccgtgtgcctcaatcgacgcggaggacacgttgatttcttatacggcgtctcag
+f2v2s20	f2v8s26	1.000000	F	863655	tggactagtagaccgtgtgcctcaatcgacgcggaggacacgttgatttcttatacggcgtctcag
+f3v3s34	f3v3s34	1.000000	T	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f4v0s44	f3v3s34	1.000000	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f3v0s31	f3v3s34	1.000000	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f0v7s7	f0v7s7	1.000000	T	515632	ggatcacacgtctatcactgctcactccaaccccggcccttgacgtccgaggagagggtgcttctgagtatgtatacccaactg
+f1v2s11	f0v7s7	1.000000	F	515632	ggatcacacgtctatcactgctcactccaaccccggcccttgacgtccgaggagagggtgcttctgagtatgtatacccaactg
+f1v1s10	f0v7s7	1.000000	F	515632	ggatcacacgtctatcactgctcactccaaccccggcccttgacgtccgaggagagggtgcttctgagtatgtatacccaactg
+f3v6s37	f3v3s34	0.973333	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgtctctaggttgttgtggctgaacgtagcact
+f5v0s53	f3v3s34	0.973333	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgtctctaggttgttgtggctgaacgtagcact
+f11v7s98	f3v3s34	0.973333	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgtctctaggttgttgtggctgaacgtagcact
+f2v4s22	f2v8s26	0.985075	F	863655	tggactagtagaccgtgtcgcctcaatcgacgcgtgaggacacgttgattcttatacggcgtctcag
+f10v7s84	f10v7s84	1.000000	T	905994	gtgccggacactcgcaatcttcacaagcagaggtccagctaacacacagcagcatttagtcccgatgggtagc
+f10v0s77	f10v7s84	0.972603	F	905994	ttgccggacactcgcaatcttccaagcagaggtccagctaacacacagcaggcatttagtcccgatgggtagc
+f5v6s59	f2v8s26	1.000000	F	863655	ggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f2v10s28	f2v8s26	1.000000	F	863655	ggactagtagaccgtgtgcctcaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f1v5s14	f0v7s7	0.961538	F	515632	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f0v4s4	f0v7s7	0.961538	F	515632	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f0v1s1	f0v7s7	0.961538	F	515632	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f0v3s3	f0v7s7	0.961538	F	515632	ggatcacagtctacactgctcactccagaccccgcccctgagtccgaggagagggtgcttcagagtatgttaccactg
+f5v3s56	f5v3s56	1.000000	T	192648	ccgcaacgcaccataagatgtaatcactaagaaaaatcggcctaacctgtcatatcgccactt
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+f4v8s52	f4v8s52	1.000000	T	368537	ctgatattcgtattgatctactacgtatcaaagtatcccacttttgtgaccccactaagagaaga
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+f3v12s43	f3v3s34	0.973684	F	838714	cgaaaaaggtgaatgaaagactgggacgcctcctggtttgggacgctctaggtggttgtggcttgaacgttagcacct
+f8v0s68	f8v0s68	1.000000	T	507278	aagaccttgaacacctctaagcgaaaattggattcgagtcagggaacataaccacgggtgcgt
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+f8v7s75	f8v0s68	0.984127	F	507278	aagaccttgaacacctctaagcgaaaattggattccagtcagggaaccataaccacgggtgcgt
+f10v12s89	f10v7s84	0.958904	F	905994	ttgccggacactcgcaatcttccaagcagaggtccagctaacacacacgcaggcatttagacccgatgggtagc
+f4v2s46	f4v8s52	0.968254	F	368537	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagagaaga
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+f11v8s99	f11v8s99	1.000000	T	421503	agcgttagcaaagagcctggttaatctgccctcgaggatcggtggtgatcagagatgcgggcatccgtttc
+f7v0s64	f7v0s64	1.000000	T	114016	gcttcgtgggaaccagagacaaccgacatatttcgaaccaccgacatacgatccttaaacc
+f11v1s92	f11v8s99	0.971429	F	421503	agcgttagcaaagagcctggttcatcgccctcgaggatcggtggtgatcaagagatgcggcatccgtttc
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+f11v0s91	f11v8s99	1.000000	F	421503	agcgttagcaaagagcctggttaatcgccctcgaggatcggtggtgatcagagatgcgggcatccgtttc
+f8v5s73	f8v0s68	0.968254	F	507278	aagaccttgtacacctctaagcgataaattggattcgagtcagggaacataaccacggatgcgt
+f8v4s72	f8v0s68	1.000000	F	507278	aagacttgaacacctctaagcgaaaattggattcgagtcagggaacataaccacgggtgcgt
+f3v1s32	f3v3s34	1.000000	F	838714	cgaaaaagagtgaatgaaatggctgggacgctcctggtttggggcgctctaggtgttgtggcttgaacgttagcacct
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+f11v6s97	f11v8s99	0.957746	F	421503	agcgttagcaaagaacctggttaatcgccctcgaggatcggtggtggatcggagatgcgggcatcgcgtttc
+f4v1s45	f4v8s52	0.938462	F	368537	ctgtatttcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactatagagaaga
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+f5v5s58	f5v3s56	0.952381	F	192648	cgcaacgcaccattaagatggtaatcactaaaaaaatcggcctaacctgtccaatcgccactt
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+f8v6s74	f8v0s68	1.000000	F	507278	aagacccttgaacacctctaagcgaaaattggattcgagtcagggaacataaccacgggtgccgt
+f6v0s60	f6v0s60	1.000000	T	100983	catgtcaagagactggaaccccggtgatgtgaaaaaaggtcttgggtacgtcccatggctacg
+f10v8s85	f10v7s84	0.945205	F	905994	ttgccggacactcgaatcttccaagcagaggtccagctaacacacagcaggcatactagtcccgatgggtagc
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+f5v4s57	f5v3s56	0.968254	F	192648	cggcaacgcaccataagatggtaatcactaaaaaaatcggcctaacctgtccatatcgccactat
+f3v10s41	f3v3s34	0.973684	F	838714	cgaaaataaggtgaatgaaagggtgggacgctcctagtttggggcgctctaggtgttgtggcttgaacgttagcacct
+f3v7s38	f3v3s34	0.986842	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggtgttcgtgcttgaacgttagcacct
+f10v6s83	f10v7s84	0.958333	F	905994	ttccggacactcgcaatcttccaagcagaggtccagctaacacacagcaggcatttagtcctgatgggtagc
+f11v2s93	f11v8s99	0.985714	F	421503	agcgttagcaaagagcctggttaatcgccctcggaggatcggtggtgatcagagatgcgggcatccgttc
+f3v9s40	f3v3s34	0.986842	F	838714	cgaaaaaggtgaatgaaaggctgggacgctcctggtttggggcgctctaggggttgtggcttgaacgttagcacct
+f11v4s95	f11v8s99	0.985507	F	421503	agcgttagcaaagagcctggttaatcccctcgagatcgggtggtgatcagagatgcgggcatccgtttc
+f8v1s69	f8v0s68	1.000000	F	507278	aagaccttgaacacctctaagcgaaaattggatatcgagtcagggaacataaccacgggtgcgt
+f11v5s96	f11v8s99	0.957746	F	421503	agcgttagcaaagagcctggttaatggccctcgaggatcggtggctgaccagagatgcgggcatccgtttc
+f6v2s62	f6v0s60	0.983871	F	100983	catgtcgagagactggaaccccggtgatgtgaaaaaaggtcttgggtacgtcccatggctac
+f4v6s50	f4v8s52	0.938462	F	368537	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagacgaagag
+f9v0s76	f9v0s76	1.000000	T	29993	gggatcgtggcaagcaacccttgccgcctcgactgcggctaaagacgcatgttccagtaataccta
+f2v12s30	f2v8s26	0.984615	F	863655	tggactagtagaccgtgtgccacaatcgacgctgaggacacgttgatttttatacggcgtctcag
+f11v9s100	f11v8s99	0.985915	F	421503	agcgttagcaaaggagcctggttaatcgccctcgaggatcggtggtgatcagagatgcgggcatccgtttc
+f4v5s49	f4v8s52	0.953125	F	368537	ctatattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagagaagca
+f2v9s27	f2v8s26	1.000000	F	863655	tggactagtagaccgtgtgcctaatcgacgcgtgaggacacgttgatttcttatacggcgtctcag
+f7v3s67	f7v0s64	1.000000	F	114016	gcttcgtgggaccagagacaaccgacatatttcgaaccaccgacatacgatccttaaacc
+f0v8s8	f0v7s7	0.974684	F	515632	ggatcacagtcctacactgctcactccaaccccggccctgagtccgaggagagggtgcttcagagtatgtataccactg
+f2v6s24	f2v8s26	0.984375	F	863655	tggactagtagacgtgtgcctcatcgacgcgtgagacactttgatttcttatacggcgtctcag
+f11v3s94	f11v8s99	0.971831	F	421503	agcgttagcaaagagcctggttaatcgccgtcgaaggatcggtggtgatcagagatgcgggcatccgtttc
+f6v3s63	f6v0s60	0.984127	F	100983	catgtcaagagactggaaccccggtgatgtgaaaaaaggttttgggtcacgtctccatggctacg
+f3v11s42	f3v3s34	0.973684	F	838714	cgaaaaaggtgaatgaaagtctgggacgctcctggtttgggacgctctaggtgttgtggcttgaacgttagcacct
+f4v4s48	f4v8s52	0.967742	F	368537	ctgtattcgtagtgatctactacgcatcaaagtatcccacttttgtaccccactaagagaaa
+f3v8s39	f3v3s34	0.986486	F	838714	cgaaaaaggtgaatgaaaggcctgggacgctcctggttggggcgctctaggtgtgtggcttgaacgttagacct
+f7v1s65	f7v0s64	0.983607	F	114016	gcttcggggaaccagagacaaccgacatatttcgaaccaccgacatacgatcctttaaacc
+f5v1s54	f5v3s56	0.952381	F	192648	cggaacgcaccataagatggtaatcactaaaaaaatcggcctaacctgtccatatcgccactt
+f4v7s51	f4v8s52	0.920635	F	368537	cgtttattcgtaggatctactacgcatcaaagtatcccacttttgtaccccactaagagcaga
+f7v2s66	f7v0s64	0.967213	F	114016	gcttcgtgggaaccagaacaaccgacatattccgaaccaccggacatacgatccttaaacc
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+f5v2s55	f5v3s56	0.936508	F	192648	cggcatcgcaccataagatggtaatcactaaaaaaatcggcctaacctgtccatatcgccact