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Fix indexing bug with "placed" unmapped reads. #1352

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Nov 12, 2021
Merged

Fix indexing bug with "placed" unmapped reads. #1352

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14 changes: 6 additions & 8 deletions hts.c
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Original file line number Diff line number Diff line change
Expand Up @@ -2384,14 +2384,12 @@ int hts_idx_push(hts_idx_t *idx, int tid, hts_pos_t beg, hts_pos_t end, uint64_t
if ( tid>=0 )
{
if (idx->bidx[tid] == 0) idx->bidx[tid] = kh_init(bin);
if (is_mapped) {
// shoehorn [-1,0) (VCF POS=0) into the leftmost bottom-level bin
if (beg < 0) beg = 0;
if (end <= 0) end = 1;
// idx->z.last_off points to the start of the current record
if (insert_to_l(&idx->lidx[tid], beg, end,
idx->z.last_off, idx->min_shift) < 0) return -1;
}
// shoehorn [-1,0) (VCF POS=0) into the leftmost bottom-level bin
if (beg < 0) beg = 0;
if (end <= 0) end = 1;
// idx->z.last_off points to the start of the current record
if (insert_to_l(&idx->lidx[tid], beg, end,
idx->z.last_off, idx->min_shift) < 0) return -1;
}
else idx->n_no_coor++;
bin = hts_reg2bin(beg, end, idx->min_shift, idx->n_lvls);
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11 changes: 11 additions & 0 deletions test/index2.sam
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@@ -0,0 +1,11 @@
@HD VN:1.4 SO:coordinate
@SQ SN:1 LN:249250621 M5:1b22b98cdeb4a9304cb5d48026a85128
@SQ SN:2 LN:243199373 M5:a0d9851da00400dec1098a9255ac712e
um1 69 1 1000000 0 * * 0 0 AAAAAAAAAA *
um1 137 1 1000000 44 10M * 0 0 AAAAAAAAAA *
um2 69 1 2000000 0 * * 0 0 AAAAAAAAAA *
um2 137 1 2000000 44 10M * 0 0 AAAAAAAAAA *
mu1 137 2 1000000 44 10M * 0 0 AAAAAAAAAA *
mu1 69 2 1000000 0 * * 0 0 AAAAAAAAAA *
mu2 137 2 2000000 44 10M * 0 0 AAAAAAAAAA *
mu2 69 2 2000000 0 * * 0 0 AAAAAAAAAA *
25 changes: 25 additions & 0 deletions test/test.pl
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Expand Up @@ -840,6 +840,31 @@ sub test_index
$wtmp =~ s/\//\\\\/g;
}
test_cmd($opts,out=>'tabix.out',cmd=>"$$opts{bin}/tabix $wtmp/index.vcf.gz##idx##$wtmp/index.vcf.gz.tbi 1:10000060-10000060");

cmd("$$opts{path}/test_view -b -p $$opts{tmp}/index2.bam -x $$opts{tmp}/index2.bam.bai $$opts{path}/index2.sam");
for (my $tid = 1; $tid <= 2; $tid++) {
for (my $pos = 1; $pos <= 2; $pos++) {
# All queries should return exactly two sequences.
# The input data consists of mapped/unmapped and unmapped/mapped
# in both orders.
# Done verbatim as test_cmd cannot return $out for us to check.
my $test = "$$opts{path}/test_view $$opts{tmp}/index2.bam $tid:${pos}000000-${pos}000000";
print "test_index:\n\t$test\n";
my ($ret, $out) = _cmd($test);
if ($ret ne 0) {
failed($opts, $test);
} else {
my $rnum = ($out =~ s/^[^@].*\n//gm);
if ($rnum ne 2) {
failed($opts, $test);
} else {
passed($opts, $test);
}
}
}
}
unlink("$$opts{tmp}/index2.bam");
unlink("$$opts{tmp}/index2.bam.bai");
}

sub test_bcf2vcf
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