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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/obiformats/fastqseq_read.go
+20 -14
View File
@@ -131,7 +131,7 @@ func _storeSequenceQuality(bytes *bytes.Buffer, out *obiseq.BioSequence, quality
out.SetQualities(q)
}
func FastqChunkParser(quality_shift byte, with_quality bool, UtoT bool) func(string, io.Reader) (obiseq.BioSequenceSlice, error) {
func FastqChunkParser(quality_shift byte, with_quality bool, UtoT bool, fileName string) func(string, io.Reader) (obiseq.BioSequenceSlice, error) {
parser := func(source string, input io.Reader) (obiseq.BioSequenceSlice, error) {
var identifier string
@@ -160,12 +160,12 @@ func FastqChunkParser(quality_shift byte, with_quality bool, UtoT bool) func(str
// Beginning of sequence
state = 1
} else {
log.Fatalf("%s : sequence entry is not starting with @", source)
log.Fatalf("file %s: sequence entry is not starting with @", fileName)
}
case 1: // Beginning of identifier (Mandatory)
if is_sep {
// No identifier -> ERROR
log.Fatalf("%s : sequence identifier is empty", source)
log.Fatalf("file %s: sequence identifier is empty", fileName)
} else {
// Beginning of identifier
state = 2
@@ -221,7 +221,7 @@ func FastqChunkParser(quality_shift byte, with_quality bool, UtoT bool) func(str
// End of sequence
rawseq := seqBytes.Bytes()
if len(rawseq) == 0 {
log.Fatalf("@%s[%s] : sequence is empty", identifier, source)
log.Fatalf("file %s: record @%s has an empty sequence line", fileName, identifier)
}
s := obiseq.NewBioSequence(identifier, rawseq, definition)
s.SetSource(source)
@@ -241,8 +241,8 @@ func FastqChunkParser(quality_shift byte, with_quality bool, UtoT bool) func(str
context = append(
append([]byte{previous}, C),
context...)
log.Fatalf("%s [%s]: sequence contains invalid character %c (%s)",
source, identifier, C, string(context))
log.Fatalf("file %s: record @%s contains invalid character %c (%s)",
fileName, identifier, C, string(context))
}
}
case 7:
@@ -251,7 +251,7 @@ func FastqChunkParser(quality_shift byte, with_quality bool, UtoT bool) func(str
} else if C == '+' {
state = 8
} else {
log.Fatalf("@%s[%s] : sequence data not followed by a line starting with + but a %c", identifier, source, C)
log.Fatalf("file %s: record @%s: sequence data not followed by a line starting with + but a %c", fileName, identifier, C)
}
case 8:
// State consuming the + internal header line
@@ -282,7 +282,7 @@ func FastqChunkParser(quality_shift byte, with_quality bool, UtoT bool) func(str
} else if C == '@' {
state = 1
} else {
log.Fatalf("%s[%s] : sequence record not followed by a line starting with @", identifier, source)
log.Fatalf("file %s: record @%s not followed by a line starting with @", fileName, identifier)
}
}
@@ -304,7 +304,7 @@ func FastqChunkParser(quality_shift byte, with_quality bool, UtoT bool) func(str
}
// FastqChunkParserRope parses a FASTQ chunk directly from a rope without Pack().
func FastqChunkParserRope(source string, rope *PieceOfChunk, quality_shift byte, with_quality, UtoT bool) (obiseq.BioSequenceSlice, error) {
func FastqChunkParserRope(source string, rope *PieceOfChunk, quality_shift byte, with_quality, UtoT bool, fileName string) (obiseq.BioSequenceSlice, error) {
scanner := newRopeScanner(rope)
sequences := obiseq.MakeBioSequenceSlice(100)[:0]
@@ -334,7 +334,7 @@ func FastqChunkParserRope(source string, rope *PieceOfChunk, quality_shift byte,
// Line 2: sequence
sline := scanner.ReadLine()
if sline == nil {
log.Fatalf("@%s[%s]: unexpected EOF after header", id, source)
log.Fatalf("file %s: record @%s is truncated (header line with no sequence line following) — the FASTQ file appears incomplete", fileName, id)
}
seqDest := make([]byte, len(sline))
w := 0
@@ -350,7 +350,7 @@ func FastqChunkParserRope(source string, rope *PieceOfChunk, quality_shift byte,
}
seqDest = seqDest[:w]
if len(seqDest) == 0 {
log.Fatalf("@%s[%s]: sequence is empty", id, source)
log.Fatalf("file %s: record @%s has an empty sequence line", fileName, id)
}
// Line 3: + (skip)
@@ -382,16 +382,17 @@ func _ParseFastqFile(
out obiiter.IBioSequence,
quality_shift byte,
with_quality, UtoT bool,
fileName string,
) {
parser := FastqChunkParser(quality_shift, with_quality, UtoT)
parser := FastqChunkParser(quality_shift, with_quality, UtoT, fileName)
for chunks := range input {
var sequences obiseq.BioSequenceSlice
var err error
if chunks.Rope != nil {
sequences, err = FastqChunkParserRope(chunks.Source, chunks.Rope, quality_shift, with_quality, UtoT)
sequences, err = FastqChunkParserRope(chunks.Source, chunks.Rope, quality_shift, with_quality, UtoT, fileName)
} else {
sequences, err = parser(chunks.Source, chunks.Raw)
}
@@ -423,6 +424,8 @@ func ReadFastq(reader io.Reader, options ...WithOption) (obiiter.IBioSequence, e
false,
)
fileName := opt.FileName()
for i := 0; i < nworker; i++ {
out.Add(1)
go _ParseFastqFile(
@@ -431,6 +434,7 @@ func ReadFastq(reader io.Reader, options ...WithOption) (obiiter.IBioSequence, e
obidefault.ReadQualitiesShift(),
opt.ReadQualities(),
opt.UtoT(),
fileName,
)
}
@@ -456,7 +460,9 @@ func ReadFastq(reader io.Reader, options ...WithOption) (obiiter.IBioSequence, e
}
func ReadFastqFromFile(filename string, options ...WithOption) (obiiter.IBioSequence, error) {
options = append(options, OptionsSource(obiutils.RemoveAllExt((path.Base(filename)))))
options = append(options,
OptionsSource(obiutils.RemoveAllExt((path.Base(filename)))),
OptionsFileName(filename))
file, err := obiutils.Ropen(filename)