Patch some bugs in writing files

Former-commit-id: 612868a281dc0ecf4e6c5776973735e5c71bd517

pkg/obiformats/fastseq_write_fasta.go

@@ -226,7 +226,10 @@ func WriteFastaToFile(iterator obiiter.IBioSequence,
 
 	if opt.AppendFile() {
 		flags |= os.O_APPEND
+	} else {
+		flags |= os.O_TRUNC
 	}
+
 	file, err := os.OpenFile(filename, flags, 0660)
 
 	if err != nil {

pkg/obiformats/fastseq_write_fastq.go

@@ -32,17 +32,31 @@ func FormatFastq(seq *obiseq.BioSequence, formater FormatHeader) string {
 		q,
 	)
 
+	if f[0] != '@' {
+		log.Panicln("FormatFastq: FASTQ format error")
+	}
+
 	return f
 }
 
 func FormatFastqBatch(batch obiiter.BioSequenceBatch,
 	formater FormatHeader, skipEmpty bool) []byte {
 	var bs bytes.Buffer
+
 	for _, seq := range batch.Slice() {
 		if seq.Len() > 0 {
 			fs := FormatFastq(seq, formater)
-			bs.WriteString(fs)
+			lb := bs.Len()
+			n, _ := bs.WriteString(fs)
+
+			if n < len(fs) {
+				log.Panicln("FormatFastqBatch: Cannot write all FASTQ sequences")
+			}
 			bs.WriteString("\n")
+
+			if bs.Len()-lb < len(fs)+1 {
+				log.Panicln("FormatFastqBatch: Cannot write all FASTQ sequences correctly")
+			}
 		} else {
 			if skipEmpty {
 				log.Warnf("Sequence %s is empty and skiped in output", seq.Id())
@@ -53,7 +67,15 @@ func FormatFastqBatch(batch obiiter.BioSequenceBatch,
 
 	}
 
-	return bs.Bytes()
+	chunk := bs.Bytes()
+
+	chunk = chunk[:bs.Len()]
+
+	if chunk[0] != '@' {
+		log.Panicln("FormatFastqBatch: FASTQ format error")
+	}
+
+	return chunk
 }
 
 type FileChunck struct {
@@ -118,16 +140,25 @@ func WriteFastq(iterator obiiter.IBioSequence,
 	go func() {
 		for chunk := range chunkchan {
 			if chunk.order == next_to_send {
+				if chunk.text[0] != '@' {
+					log.Panicln("WriteFastq: FASTQ format error")
+				}
 				file.Write(chunk.text)
 				next_to_send++
 				chunk, ok := received[next_to_send]
 				for ok {
+					if chunk.text[0] != '@' {
+						log.Panicln("WriteFastq: FASTQ format error")
+					}
 					file.Write(chunk.text)
 					delete(received, next_to_send)
 					next_to_send++
 					chunk, ok = received[next_to_send]
 				}
 			} else {
+				if _, ok := received[chunk.order]; ok {
+					log.Panicln("WriteFastq: Two chunks with the same number")
+				}
 				received[chunk.order] = chunk
 			}
 
@@ -158,7 +189,10 @@ func WriteFastqToFile(iterator obiiter.IBioSequence,
 
 	if opt.AppendFile() {
 		flags |= os.O_APPEND
+	} else {
+		flags |= os.O_TRUNC
 	}
+
 	file, err := os.OpenFile(filename, flags, 0660)
 
 	if err != nil {

pkg/obiformats/json_writer.go

@@ -174,7 +174,10 @@ func WriteJSONToFile(iterator obiiter.IBioSequence,
 
 	if opt.AppendFile() {
 		flags |= os.O_APPEND
+	} else {
+		flags |= os.O_TRUNC
 	}
+
 	file, err := os.OpenFile(filename, flags, 0660)
 
 	if err != nil {

pkg/obiformats/universal_write.go

@@ -58,7 +58,10 @@ func WriteSequencesToFile(iterator obiiter.IBioSequence,
 
 	if opt.AppendFile() {
 		flags |= os.O_APPEND
+	} else {
+		flags |= os.O_TRUNC
 	}
+
 	file, err := os.OpenFile(filename, flags, 0660)
 
 	if err != nil {

pkg/obingslibrary/multimatch.go

@@ -112,6 +112,7 @@ func lookForTag(seq string, delimiter byte) string {
 
 func lookForRescueTag(seq string, delimiter byte, taglength, border, indel int) string {
 	// log.Info("lookForRescueTag")
+	// log.Infof("seq: %s", seq)
 
 	i := len(seq) - 1
 
@@ -126,10 +127,14 @@ func lookForRescueTag(seq string, delimiter byte, taglength, border, indel int)
 		delimlen++
 	}
 
-	if obiutils.Abs(delimlen-border) > indel {
+	if (border - delimlen) > indel {
 		return ""
 	}
 
+	if delimlen > border {
+		i += delimlen - border
+	}
+
 	// log.Infof("delimlen: %d", delimlen)
 
 	end := i + 1
@@ -146,10 +151,6 @@ func lookForRescueTag(seq string, delimiter byte, taglength, border, indel int)
 		delimlen++
 	}
 
-	if obiutils.Abs(delimlen-border) > indel {
-		return ""
-	}
-
 	delimlen = min(delimlen, border)
 
 	// log.Infof("delimlen: %d", delimlen)
@@ -161,7 +162,6 @@ func lookForRescueTag(seq string, delimiter byte, taglength, border, indel int)
 	}
 
 	// log.Infof("begin: %d, end: %d", begin, end)
-	// log.Infof("seq: %s", seq)
 	// log.Infof("seq[begin:end]: %s", seq[begin:end])
 
 	return seq[begin:end]

pkg/obioptions/version.go

@@ -7,7 +7,7 @@ import (
 // TODO: The version number is extracted from git. This induces that the version
 // corresponds to the last commit, and not the one when the file will be
 // commited
-var _Commit = "1cf2768"
+var _Commit = "58bcc67"
 var _Version = "Release 4.2.0"
 
 // Version returns the version of the obitools package.

pkg/obiseq/merge.go

@@ -2,6 +2,7 @@ package obiseq
 
 import (
 	"fmt"
+	"math"
 	"reflect"
 	"strings"
 
@@ -120,8 +121,14 @@ func (sequence *BioSequence) StatsPlusOne(key string, toAdd *BioSequence, na str
 				uint8, uint16, uint32, uint64,
 				int8, int16, int32, int64, bool:
 				sval = fmt.Sprint(value)
+			case float64:
+				if math.Floor(value) == value {
+					sval = fmt.Sprint(int(value))
+				} else {
+					log.Fatalf("Trying to make stats on a float value (%v : %T)", value, value)
+				}
 			default:
-				log.Fatalf("Trying to make stats on a none string, integer or boolean value (%v)", value)
+				log.Fatalf("Trying to make stats on a none string, integer or boolean value (%v : %T)", value, value)
 			}
 			retval = true
 		}

pkg/obitools/obiconsensus/obiconsensus.go

@@ -108,14 +108,12 @@ func BuildConsensus(seqs obiseq.BioSequenceSlice,
 			sumCount += s.Count()
 		}
 
-		log.Warnf("sumCount : %d", sumCount)
+		seq.SetAttribute("obiconsensus_weight", sumCount)
-
+		seq.SetAttribute("obiconsensus_seq_length", seq.Len())
-		seq.SetCount(sumCount)
+		seq.SetAttribute("obiconsensus_kmer_size", kmer_size)
-		seq.SetAttribute("seq_length", seq.Len())
+		seq.SetAttribute("obiconsensus_kmer_max_occur", graph.MaxWeight())
-		seq.SetAttribute("kmer_size", kmer_size)
+		seq.SetAttribute("obiconsensus_filtered_graph_size", graph.Len())
-		seq.SetAttribute("kmer_max_occur", graph.MaxWeight())
+		seq.SetAttribute("obiconsensus_full_graph_size", total_kmer)
-		seq.SetAttribute("filtered_graph_size", graph.Len())
-		seq.SetAttribute("full_graph_size", total_kmer)
 	}
 	return seq, err
 }
@@ -280,19 +278,23 @@ func MinionDenoise(graph *obigraph.Graph[*obiseq.BioSequence, Mutation],
 			if err != nil {
 				log.Warning(err)
 				clean = (*graph.Vertices)[i]
-				clean.SetAttribute("obiminion_consensus", false)
+				clean.SetAttribute("obiconsensus_consensus", false)
 			} else {
-				clean.SetAttribute("obiminion_consensus", true)
+				clean.SetAttribute("obiconsensus_consensus", true)
 			}
 			pack.Recycle(false)
 		} else {
 			clean = obiseq.NewBioSequence(v.Id(), v.Sequence(), v.Definition())
-			clean.SetAttribute("obiminion_consensus", false)
+			clean.SetAttribute("obiconsensus_consensus", false)
 		}
 
-		// clean.SetCount(int(graph.VertexWeight(i)))
+		clean.SetCount(int(graph.VertexWeight(i)))
 		clean.SetAttribute(sample_key, graph.Name)
 
+		if !clean.HasAttribute("obiconsensus_weight") {
+			clean.SetAttribute("obiconsensus_weight", int(1))
+		}
+
 		denoised[i] = clean
 	}
 
@@ -376,6 +378,7 @@ func CLIOBIMinion(itertator obiiter.IBioSequence) obiiter.IBioSequence {
 	}()
 
 	obiuniq.AddStatsOn(CLISampleAttribute())
+	obiuniq.AddStatsOn("obiconsensus_weight")
 	obiuniq.SetUniqueInMemory(false)
 	obiuniq.SetNoSingleton(CLINoSingleton())
 	return obiuniq.CLIUnique(newIter).Pipe(obiiter.WorkerPipe(obiannotate.AddSeqLengthWorker(), false))