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support ##PAF lines in GFF3

This commit is contained in:
Heng Li 2022-10-07 19:34:25 -04:00
parent 5aa4355ca8
commit 2a319c89aa
1 changed files with 7 additions and 3 deletions
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10
misc/paftools.js
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@ -2422,9 +2422,11 @@ function paf_junceval(args)
var re_cigar = /(\d+)([MIDNSHP=XFGUV])/g; var re_cigar = /(\d+)([MIDNSHP=XFGUV])/g;
while (file.readline(buf) >= 0) { while (file.readline(buf) >= 0) {
var m, t = buf.toString().split("\t"); 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].charAt(0) == '@') continue;
if (t[0] == "##PAF") t.shift();
qname = t[0];
if (is_bed) { if (is_bed) {
ctg_name = t[0], pos = parseInt(t[1]), cigar == null; ctg_name = t[0], pos = parseInt(t[1]), cigar == null;
} else if (t[4] == '+' || t[4] == '-' || t[4] == '*') { // PAF } else if (t[4] == '+' || t[4] == '-' || t[4] == '*') { // PAF
@ -3308,8 +3310,10 @@ function paf_gff2junc(args) {
if (t[0][0] == '#') continue; if (t[0][0] == '#') continue;
if (t[2].toLowerCase() != feat.toLowerCase()) continue; if (t[2].toLowerCase() != feat.toLowerCase()) continue;
//print(t.join("\t")); //print(t.join("\t"));
if ((m = /\bParent=([^;]+)/.exec(t[8])) == null) if ((m = /\bParent=([^;]+)/.exec(t[8])) == null) {
throw Error("Can't find Parent"); warn("Can't find Parent");
continue;
}
t[3] = parseInt(t[3]) - 1; t[3] = parseInt(t[3]) - 1;
t[4] = parseInt(t[4]); t[4] = parseInt(t[4]);
t.unshift(m[1]); t.unshift(m[1]);