8000 int hts_detect_format(hFILE *hfile, htsFormat *fmt) can return fmt->compression = no_compression even if file is compressed · Issue #717 · samtools/htslib · GitHub
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int hts_detect_format(hFILE *hfile, htsFormat *fmt) can return fmt->compression = no_compression even if file is compressed #717

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freeseek opened this issue Jun 20, 2018 · 0 comments
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int hts_detect_format(hFILE *hfile, htsFormat *fmt) can return fmt->compression = no_compression even if file is compressed #717

freeseek opened this issue Jun 20, 2018 · 0 comments

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@freeseek
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I was trying to use int hts_detect_format(hFILE *hfile, htsFormat *fmt) from htslib/hts.h to open Illumina GTC files. These files can be either uncompressed or compressed.

However, because the first four characters of a GTC file can be "GTC\3", the execution ends up to the end of the function code:

    fmt->category = unknown_category;
    fmt->format = unknown_format;
    fmt->version.major = fmt->version.minor = -1;
    fmt->compression = no_compression;
    return 0;

And fmt->compression gets arbitrarily set to no_compression even if it is initially set to gzip. I am not going to use this function anyway, but I thought this is weird behaviour. I would just remove the second to last line from the code.
jmarshall added a commit to jmarshall/htslib that referenced this issue Jun 26, 2018
@jmarshall
Set htsFormat to unknown at the start of hts_detect_format()
ddce6b1 
Fixes samtools#717 and facilitates upcoming hts_detect_format() changes
that will mean it no longer always returns SAM for unknown data.

Also set compression_level according to XFL when CM is DEFLATE
(BGZF does not set XFL, but plain gzip does).
jmarshall added a commit to jmarshall/htslib that referenced this issue Aug 30, 2019
@jmarshall
Set htsFormat to unknown at the start of hts_detect_format()
9f03c10 
Fixes samtools#717 and facilitates upcoming hts_detect_format() changes
that will mean it no longer always returns SAM for unknown data.
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