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paftools call to show statistics on longer indels

This commit is contained in:
Heng Li 2018-07-03 14:28:09 -04:00
parent 0517972d02
commit 50dae10421
1 changed files with 11 additions and 6 deletions
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17
misc/paftools.js
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@ -340,12 +340,13 @@ function paf_liftover(args)
function paf_call(args) function paf_call(args)
{ {
var re_cs = /([:=*+-])(\d+|[A-Za-z]+)/g, re_tag = /\t(\S\S:[AZif]):(\S+)/g; var re_cs = /([:=*+-])(\d+|[A-Za-z]+)/g, re_tag = /\t(\S\S:[AZif]):(\S+)/g;
var c, min_cov_len = 10000, min_var_len = 50000, gap_thres = 50, min_mapq = 5; var c, min_cov_len = 10000, min_var_len = 50000, gap_thres = 50, gap_thres_long = 1000, min_mapq = 5;
var fa_tmp = null, fa, fa_lens, is_vcf = false; var fa_tmp = null, fa, fa_lens, is_vcf = false;
while ((c = getopt(args, "l:L:g:q:B:f:")) != null) { while ((c = getopt(args, "l:L:g:q:B:f:")) != null) {
if (c == 'l') min_cov_len = parseInt(getopt.arg); if (c == 'l') min_cov_len = parseInt(getopt.arg);
else if (c == 'L') min_var_len = parseInt(getopt.arg); else if (c == 'L') min_var_len = parseInt(getopt.arg);
else if (c == 'g') gap_thres = parseInt(getopt.arg); else if (c == 'g') gap_thres = parseInt(getopt.arg);
else if (c == 'G') gap_thres_long = parseInt(getopt.arg);
else if (c == 'q') min_mapq = parseInt(getopt.arg); else if (c == 'q') min_mapq = parseInt(getopt.arg);
else if (c == 'f') fa_tmp = fasta_read(getopt.arg, fa_lens); else if (c == 'f') fa_tmp = fasta_read(getopt.arg, fa_lens);
} }
@ -364,7 +365,7 @@ function paf_call(args)
var file = args[getopt.ind] == '-'? new File() : new File(args[getopt.ind]); var file = args[getopt.ind] == '-'? new File() : new File(args[getopt.ind]);
var buf = new Bytes(); var buf = new Bytes();
var tot_len = 0, n_sub = [0, 0, 0], n_ins = [0, 0, 0, 0], n_del = [0, 0, 0, 0]; var tot_len = 0, n_sub = [0, 0, 0], n_ins = [0, 0, 0, 0, 0], n_del = [0, 0, 0, 0, 0];
function print_vcf(o, fa) function print_vcf(o, fa)
{ {
@ -396,13 +397,15 @@ function paf_call(args)
if (l == 1) ++n_ins[0]; if (l == 1) ++n_ins[0];
else if (l == 2) ++n_ins[1]; else if (l == 2) ++n_ins[1];
else if (l < gap_thres) ++n_ins[2]; else if (l < gap_thres) ++n_ins[2];
else ++n_ins[3]; else if (l < gap_thres_long) ++n_ins[3];
else ++n_ins[4];
} else if (o[6] == '-') { // deletion } else if (o[6] == '-') { // deletion
var l = o[5].length; var l = o[5].length;
if (l == 1) ++n_del[0]; if (l == 1) ++n_del[0];
else if (l == 2) ++n_del[1]; else if (l == 2) ++n_del[1];
else if (l < gap_thres) ++n_del[2]; else if (l < gap_thres) ++n_del[2];
else ++n_del[3]; else if (l < gap_thres_long) ++n_del[3];
else ++n_del[4];
} else { } else {
++n_sub[0]; ++n_sub[0];
var s = (o[5] + o[6]).toLowerCase(); var s = (o[5] + o[6]).toLowerCase();
@ -547,8 +550,10 @@ function paf_call(args)
warn(n_ins[1] + " 2bp insertions"); warn(n_ins[1] + " 2bp insertions");
warn(n_del[2] + " [3,"+gap_thres+") deletions"); warn(n_del[2] + " [3,"+gap_thres+") deletions");
warn(n_ins[2] + " [3,"+gap_thres+") insertions"); warn(n_ins[2] + " [3,"+gap_thres+") insertions");
warn(n_del[3] + " >="+gap_thres+" deletions"); warn(n_del[3] + " ["+gap_thres+","+gap_thres_long+") deletions");
warn(n_ins[3] + " >="+gap_thres+" insertions"); warn(n_ins[3] + " ["+gap_thres+","+gap_thres_long+") insertions");
warn(n_del[4] + " >=" + gap_thres_long + " deletions");
warn(n_ins[4] + " >=" + gap_thres_long + " insertions");
buf.destroy(); buf.destroy();
file.close(); file.close();