8000 htsfile gives nonsensical results for .fq and .fq.gz files · Issue #719 · samtools/htslib · GitHub
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htsfile gives nonsensical results for .fq and .fq.gz files #719

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tseemann opened this issue Jun 22, 2018 · 1 comment
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htsfile gives nonsensical results for .fq and .fq.gz files #719

tseemann opened this issue Jun 22, 2018 · 1 comment

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@tseemann
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I do realise that htsfile does not specifically claim to work with fastq data, but i think it should be able to parse these common formats and return a correct answer:

$ htsfile reads.fq
reads.fq:       SAM version 1 sequence text

$ htsfile reads.fq.gz
reads.fq.gz:    SAM version 1 BGZF-compressed sequence data
@jmarshall
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jmarshall commented Jun 22, 2018 •
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You already reported this or something very similar as #200 😄. I must dust off my “recognise particular text formats” branch…

jmarshall added a commit to jmarshall/htslib that referenced this issue Jun 26, 2018
@jmarshall
Recognise FASTA and FASTQ files and their FAI indices
a7cb3e2 
Add htsExactFormat entries for these four file types to htslib/hts.h.

Place FASTQ in the sequence_data category as it can be considered to
be a representation of unmapped SAM. FASTA on the other hand is not,
as we don't operate on it in the same way as SAM/BAM/CRAM sequence data
and in particular we wouldn't ever want hts_open() to accept it, as
then swapping filename arguments in `samtools mpileup -f foo bar` etc
would be less detectable.

Fixes samtools#719.
jmarshall added a commit to jmarshall/htslib that referenced this issue Aug 30, 2019
@jmarshall
Recognise FASTA and FASTQ files and their FAI indices
52d72b0 
Add htsExactFormat entries for these four file types to htslib/hts.h.

Place FASTQ in the sequence_data category as it can be considered to
be a representation of unmapped SAM. FASTA on the other hand is not,
as we don't operate on it in the same way as SAM/BAM/CRAM sequence data
and in particular we wouldn't ever want hts_open() to accept it, as
then swapping filename arguments in `samtools mpileup -f foo bar` etc
would be less detectable.

Add tests verifying that FASTA and FASTQ (and SAM) can be read
line-by-line via hts_open/hts_getline/hts_close.

Fixes samtools#719.
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