--subsample option not working with writing out a FASTQ file. #85
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luispedro
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Nov 12, 2018
Many small fixes rather than any large new features. Full ChangeLog: * Fix to lock1's return value when used with paths (#68 - reopen) * Support _F/_R suffixes for forward/reverse in load_mocat_sample * samtools_sort() now accepts by={name} to sort by read name * Fixed bug where header was printed even when STDOUT was used * Fixed bug where writing interleaved FastQ to STDOUT did not work as expected * Indices created by bwa and minimap2 are now versioned * arg1 in external modules is no longer always treated as a path * Added expand_searchpath to external modules API (closes #56) * Fixed bug where detection of Fastq encoding was not performed on the second pair * Fix saving fastq sets with --subsample (issue #85) * Add __extra_megahit_args to assemble() (issue #86) * Better error message when user mis-specifies the ngless version string (issue #84) * Support NO_COLOR environment variable (issue #83) * Garbage collection for temporary files (issue #79) * Rename --search-dir to --search-path for consistency with other API * Fix corner case with select() producing incorrect CIGAR strings (#92) * Always check output file writability (#91) * Make paired() accept encoding argument
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It seems that in case of subsampling there is automatically a suffix
.subsampled
added to the output filename. While in general it is a good idea to make it obvious that it is not a full result, it backfires when ngless tries to format the filename (insertingpair.1
,pair.2
andsingles
):Which then results in the following error message:
And a small example script which results in the above error:
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