--merge works, transition to htslib completed

gpertea · gpertea · commit f687aa201a2d · 2021-06-19T11:31:55.000-04:00
diff --git a/gclib/GSam.cpp b/gclib/GSam.cpp
@@ -29,11 +29,15 @@ GSamRecord::GSamRecord(const char* qname, int32_t gseq_tid,
    b=bam_init1();
    size_t l_qname=strlen(qname);
    size_t l_seq=0;
-   if (qseq!=NULL) l_seq=strlen(qseq);
+   if (qseq!=NULL) {
+	   l_seq=strlen(qseq);
+   }
+   //-- passed pos is 1-based
    if (pos<=0 || gseq_tid<0) {
 	   flag |= BAM_FUNMAP;
 	   pos=-1;
    }
+   pos--;
    if (reverse) flag|=BAM_FREVERSE;
 
    bam_set1(b, l_qname, qname, flag,
diff --git a/gclib/GSam.h b/gclib/GSam.h
@@ -75,7 +75,7 @@ class GSamRecord: public GSeg {
 
    GSamRecord(const char* qname, int32_t gseq_tid,
            int pos, bool reverse, GDynArray<uint32_t>& cigar,
-           const char* qseq, const char* quals=NULL);
+           const char* qseq=NULL, const char* quals=NULL);
 
    void init(bam1_t* from_b, sam_hdr_t* b_header=NULL, bool adopt_b=false) {
 	   clear();
diff --git a/stringtie.cpp b/stringtie.cpp
@@ -11,7 +11,7 @@
 #include "proc_mem.h"
 #endif
 
-#define VERSION "2.1.7"
+#define VERSION "2.1.7-htslib"
 
 //#define DEBUGPRINT 1
 
diff --git a/tmerge.cpp b/tmerge.cpp
@@ -56,7 +56,7 @@ GStr TInputFiles::convert2BAM(GStr& gtf, int idx) {
 		  //cigar+='M';
 		  cigar.Add( (m.exons[k]->len() << BAM_CIGAR_SHIFT) | BAM_CMATCH);
 	  }
-	  GSamRecord brec(m.getID(), t_id, m.start, false, cigar, "*");
+	  GSamRecord brec(m.getID(), t_id, m.start, false, cigar);
 	  if (m.strand=='-' || m.strand=='+') {
 		   GStr tag("XS:A:");
 		   tag+=m.strand;

Original file line number	Diff line number	Diff line change
`@@ -56,7 +56,7 @@ GStr TInputFiles::convert2BAM(GStr& gtf, int idx) {`
`56`	`56`	`//cigar+='M';`
`57`	`57`	`cigar.Add( (m.exons[k]->len() << BAM_CIGAR_SHIFT) \| BAM_CMATCH);`
`58`	`58`	`}`
`59`		`- GSamRecord brec(m.getID(), t_id, m.start, false, cigar, "*");`
	`59`	`+ GSamRecord brec(m.getID(), t_id, m.start, false, cigar);`
`60`	`60`	`if (m.strand=='-' \|\| m.strand=='+') {`
`61`	`61`	`GStr tag("XS:A:");`
`62`	`62`	`tag+=m.strand;`