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refactor: improve FASTQ error messages with explicit filenames

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The options system now tracks explicit file paths via a new accessor and functional option. This filename is threaded through the FASTQ parser chain to replace generic source references in fatal error messages, providing clearer, file-specific diagnostics without altering core parsing logic or test suites.
This commit is contained in:
Eric Coissac
2026-08-19 16:47:36 +02:00
parent eae41ac81c
commit 438893d910
3 changed files with 67 additions and 24 deletions
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pkg/obiapat/pattern.go
+28 -10
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@@ -374,6 +374,17 @@ func (pattern ApatPattern) BestMatch(sequence ApatSequence, begin, length int) (
cpattern := (*[1 << 30]byte)(unsafe.Pointer(pattern.pointer.pointer.cpat))
frg := sequence.pointer.reference.Sequence()[start:end]
if len(frg) <= int(pattern.pointer.pointer.patlen) {
// The sequence is too short (e.g. the match is near one of its
// ends) to extract a fragment longer than the pattern, which
// obialign.LocatePattern requires. Keep the original match
// instead of refining it.
start = best[0]
end = best[1]
log.Debugln("Fragment too short for indel relocation, keeping original match", start, end, nerr)
return
}
log.Debugln(
string(frg),
string((*cpattern)[0:int(pattern.pointer.pointer.patlen)]),
@@ -480,18 +491,25 @@ func (pattern ApatPattern) AllMatches(sequence ApatSequence, begin, length int)
cpattern := (*[1 << 30]byte)(unsafe.Pointer(pattern.pointer.pointer.cpat))
frg := sequence.pointer.reference.Sequence()[start:end]
pb, pe, score := obialign.LocatePattern(
sequence.pointer.reference.Id(),
(*cpattern)[0:int(pattern.pointer.pointer.patlen)],
frg)
// obialign.LocatePattern requires the fragment to be strictly
// longer than the pattern. When the match sits near one of the
// sequence ends, the fragment can be clamped to the sequence
// boundaries and end up too short; in that case keep the
// original (unrefined) match instead of crashing.
if len(frg) > int(pattern.pointer.pointer.patlen) {
pb, pe, score := obialign.LocatePattern(
sequence.pointer.reference.Id(),
(*cpattern)[0:int(pattern.pointer.pointer.patlen)],
frg)
// olderr := m[2]
m[2] = score
m[0] = start + pb
m[1] = start + pe
// olderr := m[2]
m[2] = score
m[0] = start + pb
m[1] = start + pe
// obilog.Warnf("seq[%d@%d:%d] %d: %s %d - %s:%s:%s", i, m[0], m[1], olderr, sequence.pointer.reference.Id(), score,
// frg, (*cpattern)[0:int(pattern.pointer.pointer.patlen)], sequence.pointer.reference.Sequence()[m[0]:m[1]])
// obilog.Warnf("seq[%d@%d:%d] %d: %s %d - %s:%s:%s", i, m[0], m[1], olderr, sequence.pointer.reference.Id(), score,
// frg, (*cpattern)[0:int(pattern.pointer.pointer.patlen)], sequence.pointer.reference.Sequence()[m[0]:m[1]])
}
}
if int(pattern.pointer.pointer.maxerr) >= m[2] {