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convert MUMmer's delta to PAF

This commit is contained in:
Heng Li 2018-02-09 12:14:28 -05:00
parent 642af5591e
commit 8428809369
1 changed files with 66 additions and 1 deletions
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67
misc/paftools.js
View File

@ -840,6 +840,69 @@ function paf_sam2paf(args)
file.close();
}
function paf_delta2paf(args)
{
if (args.length == 0) {
print("Usage: paftools.js delta2paf <in.delta>");
exit(1);
}
var buf = new Bytes();
var file = args[0] == '-'? new File() : new File(args[0]);
var rname, qname, rlen, qlen, qs, qe, rs, re, strand, NM, cigar, x, y, seen_gt = false;
while (file.readline(buf) >= 0) {
var m, line = buf.toString();
if ((m = /^>(\S+)\s+(\S+)\s+(\d+)\s+(\d+)/.exec(line)) != null) {
rname = m[1], qname = m[2], rlen = parseInt(m[3]), qlen = parseInt(m[4]);
seen_gt = true;
continue;
}
if (!seen_gt) continue;
var t = line.split(" ");
if (t.length == 7) {
for (var i = 0; i < 5; ++i)
t[i] = parseInt(t[i]);
strand = ((t[0] < t[1] && t[2] < t[3]) || (t[0] > t[1] && t[2] > t[3]))? 1 : -1;
rs = (t[0] < t[1]? t[0] : t[1]) - 1;
re = t[1] > t[0]? t[1] : t[0];
qs = (t[2] < t[3]? t[2] : t[3]) - 1;
qe = t[3] > t[2]? t[3] : t[2];
x = y = 0;
NM = parseInt(t[4]);
cigar = [];
} else if (t.length == 1) {
var d = parseInt(t[0]);
if (d == 0) {
var blen = 0, cigar_str = [];
if (re - rs - x != qe - qs - y) throw Error("inconsisnt alignment");
cigar.push((re - rs - x) << 4);
for (var i = 0; i < cigar.length; ++i) {
blen += cigar[i] >> 4;
cigar_str.push((cigar[i]>>4) + "MID".charAt(cigar[i]&0xf));
}
print([qname, qlen, qs, qe, strand > 0? '+' : '-', rname, rlen, rs, re, blen - NM, blen, 0, "NM:i:" + NM, "cg:Z:" + cigar_str.join("")].join("\t"));
} else if (d > 0) {
var l = d - 1;
x += l + 1, y += l;
if (l > 0) cigar.push(l<<4);
if (cigar.length > 0 && (cigar[cigar.length-1]&0xf) == 2)
cigar[cigar.length-1] += 1<<4;
else cigar.push(1<<4|2); // deletion
} else {
var l = -d - 1;
x += l, y += l + 1;
if (l > 0) cigar.push(l<<4);
if (cigar.length > 0 && (cigar[cigar.length-1]&0xf) == 1)
cigar[cigar.length-1] += 1<<4;
else cigar.push(1<<4|1); // insertion
}
}
}
file.close();
buf.destroy();
}
function paf_splice2bed(args)
{
var colors = ["0,128,255", "255,0,0", "0,192,0"];
@ -1494,8 +1557,9 @@ function main(args)
print("Usage: paftools.js <command> [arguments]");
print("Commands:");
print(" view convert PAF to BLAST-like (for eyeballing) or MAF");
print(" sam2paf convert SAM to PAF");
print(" splice2bed convert spliced alignment in PAF/SAM to BED12");
print(" sam2paf convert SAM to PAF");
print(" delta2paf convert MUMmer's delta to PAF");
print(" gff2bed convert GTF/GFF3 to BED12");
print("");
print(" stat collect basic mapping information in PAF/SAM");
@ -1512,6 +1576,7 @@ function main(args)
var cmd = args.shift();
if (cmd == 'view') paf_view(args);
else if (cmd == 'sam2paf') paf_sam2paf(args);
else if (cmd == 'delta2paf') paf_delta2paf(args);
else if (cmd == 'splice2bed') paf_splice2bed(args);
else if (cmd == 'gff2bed') paf_gff2bed(args);
else if (cmd == 'stat') paf_stat(args);