474b9ac55dcb8e3c4cc56b00d52bd210b7989038
markd
  Thu Mar 7 22:59:45 2024 -0800
create PSLs for supplementary alignments that correct represent the query alignment.  RM: 33209

diff --git src/inc/bamFile.h src/inc/bamFile.h
index 5da2dd1..4c517c9 100644
--- src/inc/bamFile.h
+++ src/inc/bamFile.h
@@ -165,16 +165,22 @@
  * or NULL if tag is not present. */
 
 void bamUnpackAux(const bam1_t *bam, struct dyString *dy);
 /* Unpack the tag:type:val part of bam into dy */
 
 void samToBed(char *samIn, char *bedOut);
 /* samToBed - Convert SAM file to a pretty simple minded bed file.. */
 
 void samToOpenBed(char *samIn, FILE *f);
 /* Like samToOpenBed, but the output is the already open file f. */
 
 struct psl *bamToPslUnscored(const bam1_t *bam, const bam_hdr_t *hdr);
 /* Translate BAM's numeric CIGAR encoding into PSL sufficient for cds.c (just coords,
  * no scoring info) */
 
+struct psl *bamToPslUnscored2(const bam1_t *bam, const bam_hdr_t *hdr, int inclHardClipped);
+/* Translate BAM's numeric CIGAR encoding into PSL sufficient for cds.c (just coords,
+ * no scoring info).  If inclHardClipped is True, the size of the hard-clipped regions
+ * are include in the PSL.  This is required for supplementary alignments to have the
+ * correct query sizes and offsets.
+ */
 #endif//ndef BAMFILE_H