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[I/O] Small fix when reading field::cigar and changing the alignment default fields. #1642

Merged
merged 3 commits into from
Apr 24, 2020
Merged

[I/O] Small fix when reading field::cigar and changing the alignment default fields. #1642

merged 3 commits into from
Apr 24, 2020

Commits on Apr 21, 2020

  1. [FIX] Enable too-large-cigar checks when reading field::cigar. 

    If the cigar string matches ‘kSmN’ the cigar was larger then 65535 operations
and was stored in the optional CG tag of the sam_tag_dictionary.
Before this fix, the cigar string was only checked if the field::alignment was read.
    @smehringer
    smehringer committed Apr 21, 2020
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  2. [FIX] I/O: Prefer CIGAR information over alignment information in SAM… 

    …/BAM.

The alignment cannot represent hard clipping, resulting in information
loss when reading and writing SAM/BAM files if the alignment field is
preferred over the cigar field.
    @smehringer
    smehringer committed Apr 21, 2020
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  3. [FIX] I/O: Add seqan::field::cigar to the default fields. 

    Set for seqan3::alignment_file_input and seqan3::alignment_file_output.
    @smehringer
    smehringer committed Apr 21, 2020
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