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Diverse fixes and improvements - last version supporting Bowtie (1)

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@FelixKrueger FelixKrueger released this 01 Feb 14:23
· 368 commits to master since this release
0.20.1
db275a3

This is an early notice that this will be the last release of Bismark that supports the use of Bowtie 1. We have added warning statements to both the genome preparation and alignment steps to warn users that Bowtie1 is now deprecated. All Bowtie 1 functionality and support will disappear in a future release. Please shout now if you think this will be a disaster for you...

bismark

  • Added check to prevent users from inadvertently specifying the very same file as both R1 and R2

  • Added a check for file truncation, or more generally the same number of reads between R1 and R2 for paired-end FastQ files (directional, non-directional and PBAT mode).

  • Added Travis CI testing for most Bismark modules and commands. This should help spotting problems a early, e.g. if I release a new version right before the Christmas holidays ...

  • Changed error message for failed fork command in --parallel mode to [FATAL ERROR]: ... to alert users that something isn't working as intended.

bismark_genome_preparation

  • Added multi-threading to the Bowtie2-based genome preparation (thanks to Rahul Karnik)

  • Added test to see whether specified files exist, or die otherwise

bismark2summary

  • Fixed division by zero errors when a C-context was not covered by any reads. This will now use values of 0/0 for the context plots, which looks a bit odd, but at least it still works.

  • Detects if (non-deduplicated) RRBS and WGBS samples are mixed together, and bails with a meaningful error message.

bam2nuc

  • Changed samtools to $samtools_path during single-end/paired-end file testing.

bismark_methylation_extractor

  • Changed the order in which --ample_mem and --buffer_size are checked.
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