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r1053: made junceval work with PAF

This commit is contained in:
Heng Li 2021-05-26 11:54:46 -04:00
parent 41d7ccb191
commit f31705bb4a
1 changed files with 28 additions and 13 deletions
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41
misc/paftools.js
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@ -1,6 +1,6 @@
#!/usr/bin/env k8 #!/usr/bin/env k8
var paftools_version = '2.18-r1022-dirty'; var paftools_version = '2.18-r1053-dirty';
/***************************** /*****************************
***** Library functions ***** ***** Library functions *****
@ -2372,25 +2372,40 @@ function paf_junceval(args)
var re_cigar = /(\d+)([MIDNSHX=])/g; var re_cigar = /(\d+)([MIDNSHX=])/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];
if (t[0].charAt(0) == '@') continue; if (t[0].charAt(0) == '@') continue;
if (chr_only && !/^(chr)?([0-9]+|X|Y)$/.test(t[2])) continue; if (t[4] == '+' || t[4] == '-' || t[4] == '*') { // PAF
var flag = parseInt(t[1]); ctg_name = t[5], pos = parseInt(t[7]);
if (flag&0x100) continue; var type = 'P';
if (first_only && last_qname == t[0]) continue; for (i = 12; i < t.length; ++i) {
if (t[2] == '*') { if ((m = /^(tp:A|cg:Z):(\S+)/.exec(t[i])) != null) {
if (m[1] == 'tp:A') type = m[2];
else cigar = m[2];
}
}
if (type == 'S') continue; // secondary
} else { // SAM
ctg_name = t[2], pos = parseInt(t[3]) - 1, cigar = t[5];
var flag = parseInt(t[1]);
if (flag&0x100) continue; // secondary
}
if (chr_only && !/^(chr)?([0-9]+|X|Y)$/.test(ctg_name)) continue;
if (first_only && last_qname == qname) continue;
if (ctg_name == '*') { // unmapped
++n_unmapped; ++n_unmapped;
continue; continue;
} else { } else {
++n_pri; ++n_pri;
if (last_qname != t[0]) { if (last_qname != qname) {
++n_mapped; ++n_mapped;
last_qname = t[0]; last_qname = qname;
} }
} }
var pos = parseInt(t[3]) - 1, intron = []; var intron = [];
while ((m = re_cigar.exec(t[5])) != null) { while ((m = re_cigar.exec(cigar)) != null) {
var len = parseInt(m[1]), op = m[2]; var len = parseInt(m[1]), op = m[2];
if (op == 'N') { if (op == 'N') {
intron.push([pos, pos + len]); intron.push([pos, pos + len]);
@ -2403,7 +2418,7 @@ function paf_junceval(args)
} }
n_splice += intron.length; n_splice += intron.length;
var chr = anno[t[2]]; var chr = anno[ctg_name];
if (chr != null) { if (chr != null) {
for (var i = 0; i < intron.length; ++i) { for (var i = 0; i < intron.length; ++i) {
var o = Interval.find_ovlp(chr, intron[i][0], intron[i][1]); var o = Interval.find_ovlp(chr, intron[i][0], intron[i][1]);
@ -2427,12 +2442,12 @@ function paf_junceval(args)
x += '(' + o[j][0] + "," + o[j][1] + ')'; x += '(' + o[j][0] + "," + o[j][1] + ')';
} }
x += ']'; x += ']';
print(type, t[0], i+1, t[2], intron[i][0], intron[i][1], x); print(type, qname, i+1, ctg_name, intron[i][0], intron[i][1], x);
} }
} else { } else {
++n_splice_novel; ++n_splice_novel;
if (print_ovlp) if (print_ovlp)
print('N', t[0], i+1, t[2], intron[i][0], intron[i][1]); print('N', qname, i+1, ctg_name, intron[i][0], intron[i][1]);
} }
} }
} else { } else {