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Errors in BAM iterator should be fatal #265

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Merged
brentp merged 7 commits into from
Apr 1, 2026
Merged

Errors in BAM iterator should be fatal #265

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f337ba1
Use personal hts-nim fork
julianhess Mar 30, 2026
6e1e1f7
Exit nonzero if iterator fails due to IO issues
julianhess Mar 30, 2026
5f89f63
Merge branch 'build-update'
julianhess Mar 31, 2026
b88f7eb
Bump hts-nim dependency version
julianhess Mar 31, 2026
19ff805
IOError -> BamError
julianhess Mar 31, 2026
cebeec2
Revert "Use personal hts-nim fork"
julianhess Apr 1, 2026
3207a70
Add comment clarifying try/except block
julianhess Apr 1, 2026
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10 changes: 8 additions & 2 deletions mosdepth.nim
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Original file line number Diff line number Diff line change
Expand Up @@ -181,8 +181,14 @@ iterator regions(bam: hts.Bam, region: region_t, tid: int, targets: seq[
if tid != -1:
if stop == 0:
stop = targets[tid].length
for r in bam.query(tid, int(region.start), int(stop)):
yield r
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brentp marked this conversation as resolved.
try:
for r in bam.query(tid, int(region.start), int(stop)):
yield r
# if the iterator fails due to an invalid read from the BAM (due to file
# corruption or filesystem issues), we want to gracefully exit with a
# nonzero return.
except hts.BamError:
quit getCurrentExceptionMsg()
else:
stderr.write_line("[mosdepth]", region.chrom, " not found")

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2 changes: 1 addition & 1 deletion mosdepth.nimble
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Expand Up @@ -7,7 +7,7 @@ license = "MIT"

# Dependencies

requires "hts >= 0.3.29", "docopt == 0.7.1", "nim >= 1.0.0", "https://github.com/brentp/d4-nim >= 0.0.5"
requires "hts >= 0.3.31", "docopt == 0.7.1", "nim >= 1.0.0", "https://github.com/brentp/d4-nim >= 0.0.5"

bin = @["mosdepth"]
skipDirs = @["tests"]
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