First commit

pkg/obiformats/fastseq_read.go

@@ -0,0 +1,153 @@
+package obiformats
+
+// #cgo CFLAGS: -g -Wall
+// #cgo LDFLAGS: -lz
+// #include <stdlib.h>
+// #include "fastseq_read.h"
+import "C"
+
+import (
+	"errors"
+	"fmt"
+	"log"
+	"os"
+	"time"
+	"unsafe"
+
+	"git.metabarcoding.org/lecasofts/go/oa2/pkg/cutils"
+	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+)
+
+func __fastseq_reader__(seqfile C.fast_kseq_p,
+	iterator obiseq.IBioSequenceBatch,
+	batch_size int) {
+	var comment string
+	i := 0
+	ii := 0
+
+	slice := make(obiseq.BioSequenceSlice, 0, batch_size)
+
+	for l := int64(C.next_fast_sek(seqfile)); l > 0; l = int64(C.next_fast_sek(seqfile)) {
+
+		s := seqfile.seq
+
+		sequence := C.GoBytes(unsafe.Pointer(s.seq.s),
+			C.int(s.seq.l))
+
+		name := C.GoString(s.name.s)
+
+		if s.comment.l > C.ulong(0) {
+			comment = C.GoString(s.comment.s)
+		} else {
+			comment = ""
+		}
+
+		rep := obiseq.MakeBioSequence(name, sequence, comment)
+
+		if s.qual.l > C.ulong(0) {
+			cquality := cutils.ByteSlice(unsafe.Pointer(s.qual.s), int(s.qual.l))
+			quality := make(obiseq.Quality, s.qual.l)
+			l := int(s.qual.l)
+			shift := uint8(seqfile.shift)
+			for j := 0; j < l; j++ {
+				quality[j] = uint8(cquality[j]) - shift
+			}
+
+			rep.SetQualities(quality)
+		}
+		slice = append(slice, rep)
+		ii++
+		if ii >= batch_size {
+			// log.Printf("\n==> Pushing sequence batch\n")
+			// start := time.Now()
+
+			iterator.Channel() <- obiseq.MakeBioSequenceBatch(i, slice...)
+			// elapsed := time.Since(start)
+			// log.Printf("\n==>sequences pushed after %s\n", elapsed)
+
+			slice = make(obiseq.BioSequenceSlice, 0, batch_size)
+			i++
+			ii = 0
+		}
+	}
+	if len(slice) > 0 {
+		iterator.Channel() <- obiseq.MakeBioSequenceBatch(i, slice...)
+	}
+	iterator.Done()
+
+}
+
+func ReadFastSeqBatchFromFile(filename string, options ...WithOption) (obiseq.IBioSequenceBatch, error) {
+	opt := MakeOptions(options)
+
+	name := C.CString(filename)
+	defer C.free(unsafe.Pointer(name))
+
+	pointer := C.open_fast_sek_file(name, C.int32_t(opt.QualityShift()))
+
+	var err error
+	err = nil
+
+	if pointer == nil {
+		err = errors.New(fmt.Sprintf("Cannot open file %s", filename))
+		return obiseq.NilIBioSequenceBatch, err
+	}
+
+	size := int64(-1)
+	fi, err := os.Stat(filename)
+	if err == nil {
+		size = fi.Size()
+		log.Printf("File size of %s is %d bytes\n", filename, size)
+	} else {
+		size = -1
+	}
+
+	new_iter := obiseq.MakeIBioSequenceBatch(opt.BufferSize())
+	new_iter.Add(1)
+
+	go func() {
+		new_iter.Wait()
+		for len(new_iter.Channel()) > 0 {
+			time.Sleep(time.Millisecond)
+		}
+		close(new_iter.Channel())
+
+		log.Println("End of the fastq file reading")
+	}()
+
+	log.Println("Start of the fastq file reading")
+
+	go __fastseq_reader__(pointer, new_iter, opt.BatchSize())
+	parser := opt.ParseFastSeqHeader()
+	if parser != nil {
+		return IParseFastSeqHeaderBatch(new_iter, options...), err
+	}
+
+	return new_iter, err
+}
+
+func ReadFastSeqFromFile(filename string, options ...WithOption) (obiseq.IBioSequence, error) {
+	ib, err := ReadFastSeqBatchFromFile(filename, options...)
+	return ib.SortBatches().IBioSequence(), err
+}
+
+func ReadFastSeqBatchFromStdin(options ...WithOption) obiseq.IBioSequenceBatch {
+	opt := MakeOptions(options)
+	new_iter := obiseq.MakeIBioSequenceBatch(opt.BufferSize())
+
+	new_iter.Add(1)
+
+	go func() {
+		new_iter.Wait()
+		close(new_iter.Channel())
+	}()
+
+	go __fastseq_reader__(C.open_fast_sek_stdin(C.int32_t(opt.QualityShift())), new_iter, opt.BatchSize())
+
+	return new_iter
+}
+
+func ReadFastSeqFromStdin(options ...WithOption) obiseq.IBioSequence {
+	ib := ReadFastSeqBatchFromStdin(options...)
+	return ib.SortBatches().IBioSequence()
+}