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bismark2bedGraph fails to sort GZIP compressed files #9

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FelixKrueger opened this issue Dec 9, 2015 · 1 comment
Closed

bismark2bedGraph fails to sort GZIP compressed files #9

FelixKrueger opened this issue Dec 9, 2015 · 1 comment

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@FelixKrueger
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It appears the bismark2bedGraph produces empty coverage files when using the command line

bismark2bedGraph --dir /Path_to_dir --buffer_size 10G --scaffolds -o CpG_file.bed.gz /path_to_dir/CpG_context_file.fastq.gz_bismark_pe.deduplicated.sorted.txt.gz
@FelixKrueger
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I have looked into this and it appears that the files were opened as a stream from the Unix sort command, however sort cannot read gzip compressed files. As a result the stream from sort is just empty. I have now changed this to a zcat stream piped into sort, and it seems to be working well on my end now. Addressed in 271c00f.

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@FelixKrueger