Merge pull request #3033 from nsoranzo/fix_for_3001

Increase min number of columns for pileup sniffing to 5
2026-09-24 16:30:27 +08:00 · 2016-10-17 13:23:40 -04:00
parent 4bf1994fc3 3be66005dc
commit 7207c15090
1 changed files with 3 additions and 2 deletions
@@ -644,12 +644,13 @@ class Pileup( Tabular ):
        try:
            for hdr in headers:
                if hdr and not hdr[0].startswith( '#' ):
-                    if len( hdr ) < 3:
+                    if len( hdr ) < 5:
                        return False
                    try:
                        # chrom start in column 1 (with 0-based columns)
                        # and reference base is in column 2
-                        int( hdr[1] )
+                        chrom = int( hdr[1] )
+                        assert chrom >= 0
                        assert hdr[2] in [ 'A', 'C', 'G', 'T', 'N', 'a', 'c', 'g', 't', 'n' ]
                    except:
                        return False