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removed altlift; suppress primary hit by default

This commit is contained in:
Heng Li 2014-09-19 17:05:27 -04:00
parent 7426a750ec
commit 23bc50e240
1 changed files with 6 additions and 71 deletions
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77
bwa-helper.js
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@ -522,14 +522,15 @@ function read_ALT_sam(fn)
function bwa_altgen(args) function bwa_altgen(args)
{ {
var c, opt = { a:1, b:4, o:6, e:1, verbose:3 }; var c, opt = { a:1, b:4, o:6, e:1, verbose:3, show_pri:false };
while ((c = getopt(args, 'v:')) != null) { while ((c = getopt(args, 'pv:')) != null) {
if (c == 'v') opt.verbose = parseInt(getopt.arg); if (c == 'v') opt.verbose = parseInt(getopt.arg);
else if (c == 'p') opt.show_pri = true;
} }
if (args.length == getopt.ind) { if (args.length == getopt.ind) {
print("Usage: k8 bwa-helper.js altgen <alt.sam> [aln.sam]"); print("Usage: k8 bwa-helper.js altgen [-p] <alt.sam> [aln.sam]");
exit(1); exit(1);
} }
@ -671,6 +672,7 @@ function bwa_altgen(args)
for (var i = 0; i < hits.length; ++i) { for (var i = 0; i < hits.length; ++i) {
if (opt.verbose >= 5) print(obj2str(hits[i])); if (opt.verbose >= 5) print(obj2str(hits[i]));
if (hits[i].g != reported_g || i == reported_i) continue; if (hits[i].g != reported_g || i == reported_i) continue;
if (!opt.show_pri && idx[hits[i].ctg] == null) continue;
var s = [t[0], flag&0xf10, hits[i].ctg, hits[i].start+1, mapQ, hits[i].cigar, '*', 0, 0]; var s = [t[0], flag&0xf10, hits[i].ctg, hits[i].start+1, mapQ, hits[i].cigar, '*', 0, 0];
// update name // update name
if (flag&0x40) s[0] += "/1"; if (flag&0x40) s[0] += "/1";
@ -689,71 +691,6 @@ function bwa_altgen(args)
buf.destroy(); buf.destroy();
} }
// This is in effect a simplified version of bwa_genalt().
function bwa_altlift(args)
{
var opt = { a:1, b:4, o:6, e:1 };
if (args.length == 0) {
print("Usage: k8 bwa-helper.js altlift <alt-to-ref.sam> [aln.sam]");
exit(1);
}
var idx = read_ALT_sam(args[0]);
// process SAM
var file = args.length >= 2? new File(args[1]) : new File();
var buf = new Bytes();
while (file.readline(buf) >= 0) {
var m, line = buf.toString();
if (line.charAt(0) == '@') {
print(line);
continue;
}
var t = line.split("\t");
var NM = (m = /\tNM:i:(\d+)/.exec(line)) == null? '0' : m[1];
var flag = parseInt(t[1]);
var h = parse_hit([t[2], ((flag&16)?'-':'+') + t[3], t[5], NM], opt);
// lift mapping positions to coordinates on the primary assembly
var a = null;
if (idx[h.ctg] != null)
a = idx[h.ctg](h.start, h.end);
if (a == null) a = [];
// find the approximate position on the primary assembly
var lifted = [];
for (var j = 0; j < a.length; ++j) {
var s, e;
if (!a[j][4]) { // ALT is mapped to the forward strand of the primary assembly
s = cigar2pos(a[j][6], h.start);
e = cigar2pos(a[j][6], h.end - 1) + 1;
} else {
s = cigar2pos(a[j][6], a[j][2] - h.end);
e = cigar2pos(a[j][6], a[j][2] - h.start - 1) + 1;
}
if (s < 0 || e < 0) continue; // read is mapped to clippings in the ALT-to-chr alignment
s += a[j][5]; e += a[j][5];
lifted.push([a[j][3], (h.rev!=a[j][4]), s, e]);
}
h.lifted = lifted;
// generate lifted_str
if (h.lifted && h.lifted.length) {
var lifted = h.lifted;
var u = '';
for (var j = 0; j < lifted.length; ++j)
u += lifted[j][0] + "," + lifted[j][2] + "," + lifted[j][3] + "," + (lifted[j][1]?'-':'+') + ";";
h.lifted_str = u;
} else h.lifted_str = null;
// print
if (h.lifted_str) t.push("lt:Z:" + h.lifted_str);
print(t.join("\t"));
}
buf.destroy();
file.close();
}
/********************* /*********************
*** Main function *** *** Main function ***
*********************/ *********************/
@ -762,8 +699,7 @@ function main(args)
{ {
if (args.length == 0) { if (args.length == 0) {
print("\nUsage: k8 bwa-helper.js <command> [arguments]\n"); print("\nUsage: k8 bwa-helper.js <command> [arguments]\n");
print("Commands: altlift add lt tag to show lifted position on the primary assembly"); print("Commands: altgen generate ALT alignments for ALT-unaware alignments");
print(" altgen generate ALT alignments for ALT-unaware alignments\n");
print(" sam2pas convert SAM to pairwise alignment summary format (PAS)"); print(" sam2pas convert SAM to pairwise alignment summary format (PAS)");
print(" pas2reg extract covered regions"); print(" pas2reg extract covered regions");
print(" reg2cut regions to extract for the 2nd round bwa-mem"); print(" reg2cut regions to extract for the 2nd round bwa-mem");
@ -781,7 +717,6 @@ function main(args)
else if (cmd == 'pas2reg') bwa_pas2reg(args); else if (cmd == 'pas2reg') bwa_pas2reg(args);
else if (cmd == 'reg2cut') bwa_reg2cut(args); else if (cmd == 'reg2cut') bwa_reg2cut(args);
else if (cmd == 'altgen' || cmd == 'genalt') bwa_altgen(args); else if (cmd == 'altgen' || cmd == 'genalt') bwa_altgen(args);
else if (cmd == 'altlift') bwa_altlift(args);
else if (cmd == 'shortname') bwa_shortname(args); else if (cmd == 'shortname') bwa_shortname(args);
else warn("Unrecognized command"); else warn("Unrecognized command");
} }