From 85a5260408cf0291f3659d5107e475403f98d5bf Mon Sep 17 00:00:00 2001 From: Heng Li Date: Fri, 7 Oct 2022 19:33:27 -0400 Subject: [PATCH] correctly parse ##PAF lines in GFF3 (for miniprot) --- misc/paftools.js | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/misc/paftools.js b/misc/paftools.js index b2d4b28..6a186b4 100755 --- a/misc/paftools.js +++ b/misc/paftools.js @@ -2422,9 +2422,11 @@ function paf_junceval(args) var re_cigar = /(\d+)([MIDNSHP=XFGUV])/g; while (file.readline(buf) >= 0) { var m, t = buf.toString().split("\t"); - var ctg_name = null, cigar = null, pos = null, qname = t[0]; + var ctg_name = null, cigar = null, pos = null, qname; if (t[0].charAt(0) == '@') continue; + if (t[0] == "##PAF") t.shift(); + qname = t[0]; if (is_bed) { ctg_name = t[0], pos = parseInt(t[1]), cigar == null; } else if (t[4] == '+' || t[4] == '-' || t[4] == '*') { // PAF