From 65210755cc2b66a0bcf0f141a703f301d5a2a85e Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Thu, 29 Sep 2022 14:48:05 +0200
Subject: [PATCH] Patch reading of annotation from stdin

---
 pkg/obiformats/fastseq_read.c              |  4 ++++
 pkg/obiformats/fastseq_read.go             | 12 ++++++++++--
 pkg/obitools/obiconvert/sequence_reader.go |  6 +++---
 3 files changed, 17 insertions(+), 5 deletions(-)

diff --git a/pkg/obiformats/fastseq_read.c b/pkg/obiformats/fastseq_read.c
index 5a06a45..a4bccaa 100644
--- a/pkg/obiformats/fastseq_read.c
+++ b/pkg/obiformats/fastseq_read.c
@@ -52,6 +52,7 @@ fast_kseq_p open_fast_sek_fd(int fd, bool keep_open, int shift) {
         fd = dup(fd);
 
     fp = gzdopen(fd, "r"); 
+
     return _open_fast_sek(fp, shift);
 }
 
@@ -67,8 +68,11 @@ int64_t next_fast_sek(fast_kseq_t* iterator) {
         return -3;
 
     l = kseq_read(iterator->seq);
+    if (l < 0) l = 0;
+
     iterator->finished = l==0;
     if (l>0) l = gzoffset(iterator->filez);
+
     return l;
 }
 
diff --git a/pkg/obiformats/fastseq_read.go b/pkg/obiformats/fastseq_read.go
index 0b3ee7c..372cd69 100644
--- a/pkg/obiformats/fastseq_read.go
+++ b/pkg/obiformats/fastseq_read.go
@@ -26,8 +26,7 @@ func _FastseqReader(seqfile C.fast_kseq_p,
 
 	slice := obiseq.MakeBioSequenceSlice()
 
-	for l := int64(C.next_fast_sek(seqfile)); l > 0; l = int64(C.next_fast_sek(seqfile)) {
-
+	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))
@@ -77,6 +76,9 @@ func _FastseqReader(seqfile C.fast_kseq_p,
 			i++
 			ii = 0
 		}
+
+		// log.Println("longueur : ",l,rep.Length())
+
 	}
 	if len(slice) > 0 {
 		iterator.Push(obiiter.MakeBioSequenceBatch(i, slice))
@@ -148,6 +150,12 @@ func ReadFastSeqBatchFromStdin(options ...WithOption) obiiter.IBioSequenceBatch
 	go _FastseqReader(C.open_fast_sek_stdin(C.int32_t(opt.QualityShift())),
 		newIter, opt.BatchSize())
 
+	parser := opt.ParseFastSeqHeader()
+
+	if parser != nil {
+		return IParseFastSeqHeaderBatch(newIter, options...)
+	}
+
 	return newIter
 }
 
diff --git a/pkg/obitools/obiconvert/sequence_reader.go b/pkg/obitools/obiconvert/sequence_reader.go
index 6ab8fca..8a29e96 100644
--- a/pkg/obitools/obiconvert/sequence_reader.go
+++ b/pkg/obitools/obiconvert/sequence_reader.go
@@ -82,7 +82,7 @@ func ReadBioSequencesBatch(filenames ...string) (obiiter.IBioSequenceBatch, erro
 		opts = append(opts, obiformats.OptionsFastSeqHeaderParser(obiformats.ParseGuessedFastSeqHeader))
 	}
 
-	nworkers := obioptions.CLIParallelWorkers() / 4
+	nworkers := obioptions.CLIParallelWorkers() // / 4
 	if nworkers < 2 {
 		nworkers = 2
 	}
@@ -94,7 +94,7 @@ func ReadBioSequencesBatch(filenames ...string) (obiiter.IBioSequenceBatch, erro
 	opts = append(opts, obiformats.OptionsQualityShift(CLIInputQualityShift()))
 
 	if len(filenames) == 0 {
-
+		log.Printf("Reading sequences from stdin in %s\n", CLIInputFormat())
 		switch CLIInputFormat() {
 		case "ecopcr":
 			iterator = obiformats.ReadEcoPCRBatch(os.Stdin, opts...)
@@ -129,7 +129,7 @@ func ReadBioSequencesBatch(filenames ...string) (obiiter.IBioSequenceBatch, erro
 			if CLINoInputOrder() {
 				nreader = obioptions.CLIParallelWorkers()
 			}
-			
+
 			iterator = obiformats.ReadSequencesBatchFromFiles(
 				filenames,
 				reader,