ZStandard compression breaks saving BAM files

ngless-toolkit / ngless

NGLess: NGS with less work

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ZStandard compression breaks saving BAM files #103

Closed unode closed 5 years ago

unode commented 5 years ago

write(ofile="output.bam") fails with:

[Fri 01-03-2019 00:05:46] Line 11: Created & opened temporary file /tmp/converted_mapped_ref64446-6.bam
[Fri 01-03-2019 00:05:46] Line 11: SAM->BAM Conversion start ('/tmp/mapped_ref..sam64446-0.zstd' -> '/tmp/converted_mapped_ref64446-6.bam')
[Fri 01-03-2019 00:05:46] Line 11: Message from samtools: [W::sam_read1] Parse error at line 1
[main_samview] truncated file.

This fails because samtools doesn't know how to handle a zstd file.

unode commented 5 years ago

Possibly related, .gz outputs are actually .zstd files.

luispedro commented 5 years ago

I will consider this a bug of our test suite for not having caught it before!