optionally mark multi-part hits as secondary

nh13 · Nov 24, 2011 · 196b50d · 196b50d
1 parent 9f84384
commit 196b50d
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/bwtsw2_aux.c b/bwtsw2_aux.c
@@ -489,7 +489,7 @@ static void print_hits(const bntseq_t *bns, const bsw2opt_t *opt, bsw2seq1_t *ks
 		bsw2aux_t *q = b->aux + i;
 		int j, beg, end, type = 0;
 		// print mandatory fields before SEQ
-		ksprintf(&str, "%s\t%d", ks->name, q->flag);
+		ksprintf(&str, "%s\t%d", ks->name, q->flag | (opt->multi_2nd && i? 0x100 : 0));
 		ksprintf(&str, "\t%s\t%ld", q->chr>=0? bns->anns[q->chr].name : "*", (long)q->pos + 1);
 		if (p->l == 0) { // not a repetitive hit
 			ksprintf(&str, "\t%d\t", q->pqual);

diff --git a/main.c b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.6.0-r91-dev"
+#define PACKAGE_VERSION "0.6.0-r97-dev"
 #endif
 
 static int usage()