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r907: copy tag "cs" in sam2paf 

Resolves #310
This commit is contained in:
Heng Li 2019-01-13 17:52:31 -05:00
parent 48e230f40d
commit 30abcf3cf9
1 changed files with 7 additions and 5 deletions
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12
misc/paftools.js
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@ -1,6 +1,6 @@
#!/usr/bin/env k8
var paftools_version = '2.15-r905';
var paftools_version = '2.15-r907-dirty';
/*****************************
***** Library functions *****
@ -1623,13 +1623,14 @@ function paf_sam2paf(args)
var tlen = ctg_len[t[2]];
if (tlen == null) throw Error("at line " + lineno + ": can't find the length of contig " + t[2]);
// find tags
var nn = 0, NM = null, MD = null, md_list = [];
var nn = 0, NM = null, MD = null, cs_str = null, md_list = [];
while ((m = re_tag.exec(line)) != null) {
if (m[1] == "NM:i") NM = parseInt(m[2]);
else if (m[1] == "nn:i") nn = parseInt(m[2]);
else if (m[1] == "MD:Z") MD = m[2];
else if (m[1] == "cs:Z") cs_str = m[2];
}
if (t[9] == '*') MD = null;
if (t[9] == '*') MD = cs_str = null;
// infer various lengths from CIGAR
var clip = [0, 0], soft_clip = 0, I = [0, 0], D = [0, 0], M = 0, N = 0, mm = 0, have_M = false, have_ext = false, cigar = [];
while ((m = re.exec(t[5])) != null) {
@ -1665,7 +1666,7 @@ function paf_sam2paf(args)
}
// parse MD
var cs = [];
if (MD != null) {
if (MD != null && cs_str == null) {
var k = 0, cx = 0, cy = 0, mx = 0, my = 0;
while ((m = re_MD.exec(MD)) != null) {
if (m[2] != null) { // deletion from the reference
@ -1731,7 +1732,8 @@ function paf_sam2paf(args)
var tags = ["tp:A:" + type];
if (NM != null) tags.push("mm:i:"+mm);
tags.push("gn:i:"+(I[1]+D[1]), "go:i:"+(I[0]+D[0]), "cg:Z:" + t[5].replace(/\d+[SH]/g, ''));
if (cs.length > 0) tags.push("cs:Z:" + cs.join(""));
if (cs_str != null) tags.push("cs:Z:" + cs_str);
else if (cs.length > 0) tags.push("cs:Z:" + cs.join(""));
// print out
var a = [qname, qlen, qs, qe, flag&16? '-' : '+', t[2], tlen, ts, te, mlen, blen, t[4]];
print(a.join("\t"), tags.join("\t"));