[view] Support extra int type encodings for auxiliary tags (PR #1370)

samtools · Feb 8, 2021 · 2257c57 · 2257c57
1 parent 4d05eaa
commit 2257c57
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/sam_view.c b/sam_view.c
@@ -1,6 +1,6 @@
 /*  sam_view.c -- SAM<->BAM<->CRAM conversion.
 
-    Copyright (C) 2009-2020 Genome Research Ltd.
+    Copyright (C) 2009-2021 Genome Research Ltd.
     Portions copyright (C) 2009, 2011, 2012 Broad Institute.
 
     Author: Heng Li <lh3@sanger.ac.uk>
@@ -107,7 +107,7 @@ static int process_aln(const sam_hdr_t *h, bam1_t *b, samview_settings_t* settin
         if (s) {
             if (settings->tvhash) {
                 char t[32], *val;
-                if (*s == 'i' || *s == 'I' || *s == 'c' || *s == 'C') {
+                if (*s == 'i' || *s == 'I' || *s == 's' || *s == 'S' || *s == 'c' || *s == 'C') {
                     int ret = snprintf(t, 32, "%"PRId64, bam_aux2i(s));
                     if (ret > 0) val = t;
                     else return 1;

diff --git a/test/test.pl b/test/test.pl
@@ -1198,7 +1198,7 @@ sub filter_sam
                 if ($tag_values) {
                     my $tag_value = '';
                     for my $i (11 .. $#sam) {
-                        last if (($tag_value) = $sam[$i] =~ /^${tag}:[ZiIcC]:(.*)/);
+                        last if (($tag_value) = $sam[$i] =~ /^${tag}:[ZiIsScC]:(.*)/);
                     }
                     next if (!exists($tag_values->{$tag_value||""}));
                 }