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r755: junceval to only evaluate chromosomes

This commit is contained in:
Heng Li 2018-03-24 23:10:06 -04:00
parent 1c504d72e4
commit 0bf97a367b
1 changed files with 6 additions and 3 deletions
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9
misc/paftools.js
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@ -1,6 +1,6 @@
#!/usr/bin/env k8 #!/usr/bin/env k8
var paftools_version = 'r754'; var paftools_version = 'r755';
/***************************** /*****************************
***** Library functions ***** ***** Library functions *****
@ -1758,11 +1758,12 @@ function paf_pbsim2fq(args)
function paf_junceval(args) function paf_junceval(args)
{ {
var c, l_fuzzy = 0, print_ovlp = false, print_err_only = false, first_only = false; var c, l_fuzzy = 0, print_ovlp = false, print_err_only = false, first_only = false, chr_only = false;
while ((c = getopt(args, "l:ep")) != null) { while ((c = getopt(args, "l:epc")) != null) {
if (c == 'l') l_fuzzy = parseInt(getopt.arg); if (c == 'l') l_fuzzy = parseInt(getopt.arg);
else if (c == 'e') print_err_only = print_ovlp = true; else if (c == 'e') print_err_only = print_ovlp = true;
else if (c == 'p') print_ovlp = true; else if (c == 'p') print_ovlp = true;
else if (c == 'c') chr_only = true;
} }
if (args.length - getopt.ind < 1) { if (args.length - getopt.ind < 1) {
@ -1771,6 +1772,7 @@ function paf_junceval(args)
print(" -l INT tolerance of junction positions (0 for exact) [0]"); print(" -l INT tolerance of junction positions (0 for exact) [0]");
print(" -p print overlapping introns"); print(" -p print overlapping introns");
print(" -e print erroreous overlapping introns"); print(" -e print erroreous overlapping introns");
print(" -c only consider alignments to /^(chr)?([0-9]+|X|Y)$/");
exit(1); exit(1);
} }
@ -1829,6 +1831,7 @@ function paf_junceval(args)
var m, t = buf.toString().split("\t"); var m, t = buf.toString().split("\t");
if (t[0].charAt(0) == '@') continue; if (t[0].charAt(0) == '@') continue;
if (chr_only && !/^(chr)?([0-9]+|X|Y)$/.test(t[2])) continue;
var flag = parseInt(t[1]); var flag = parseInt(t[1]);
if (flag&0x100) continue; if (flag&0x100) continue;
if (first_only && last_qname == t[0]) continue; if (first_only && last_qname == t[0]) continue;