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Merged
pull merged 1 commit into from
Oct 6, 2025
Merged

[pull] master from lh3:master #144

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16 changes: 13 additions & 3 deletions misc/paftools.js
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Original file line number Diff line number Diff line change
Expand Up @@ -1740,17 +1740,19 @@ function paf_gff2bed(args)

function paf_sam2paf(args)
{
var c, pri_only = false, long_cs = false, pri_pri_only = false;
while ((c = getopt(args, "pPL")) != null) {
var c, pri_only = false, long_cs = false, pri_pri_only = false, allow_unmapped = false;
while ((c = getopt(args, "pPUL")) != null) {
if (c == 'p') pri_only = true;
else if (c == 'P') pri_pri_only = pri_only = true;
else if (c == 'U') allow_unmapped = true;
else if (c == 'L') long_cs = true;
}
if (args.length == getopt.ind) {
print("Usage: paftools.js sam2paf [options] <in.sam>");
print("Options:");
print(" -p convert primary or supplementary alignments only");
print(" -P convert primary alignments only");
print(" -U convert unmapped reads as well");
print(" -L output the cs tag in the long form");
exit(1);
}
Expand All @@ -1775,7 +1777,15 @@ function paf_sam2paf(args)
var flag = parseInt(t[1]);
if (t[9] != '*' && t[10] != '*' && t[9].length != t[10].length)
throw Error("at line " + lineno + ": inconsistent SEQ and QUAL lengths - " + t[9].length + " != " + t[10].length);
if (t[2] == '*' || (flag&4) || t[5] == '*') continue;
if (t[2] == '*' || (flag&4) || t[5] == '*') {
if (allow_unmapped) {
// emit an unmapped PAF line instead of skipping
// fields: qname, qlen, qstart, qend, strand, tname, tlen, tstart, tend, n_match, aln_len, mapq
var qlen_val = (t[9] == '*' ? 0 : t[9].length);
print([t[0], qlen_val, 0, 0, '*', '*', 0, 0, 0, 0, 0, 0].join("\t"));
}
continue;
}
if (pri_only && (flag&0x100)) continue;
if (pri_pri_only && (flag&0x900)) continue;
var tlen = ctg_len[t[2]];
Expand Down