Charles Plessy e75f88c68a New module last/mafswap to reorder sequences in alignments (#500) ... * New module last/mafswap to reorder sequences in alignments The `maf-swap` tool distributed with [LAST](https://gitlab.com/mcfrith/last) reorders sequences in alignment files in Multiple Alignment Format. When run without command-line arguments, it will swap the target and the query sequences. This is useful when turning a many-to-many alignment into a many-to-one and then a one-to-one alignment in conjunction with the `last-split` command (split, swap, split and swap again). The LAST aligner outputs MAF files, but other tools also use this format. As MAF files can be very large (up to hundreds of gigabytes), the module expects its input to be compressed with gzip and will compress its output. This new module is part of the work described in Issue #464. During this development, we fix the version of LAST to 1219 to ensure consistency (hence ignore lint's version warning). * Update MD5 sum. Actually, 7029066c27ac6f5ef18d660d5741979a is the MD5 sum of an empty file compressed with `gzip --no-name`… This happened because I forgot to update the config file after correcting the module… sorry ! * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Change name as suggested in pull request. Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>		2021-05-19 08:59:23 +01:00
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lastdb	Update comments with new style (#497)	2021-05-12 14:56:46 +01:00
mafswap	New module last/mafswap to reorder sequences in alignments (#500)	2021-05-19 08:59:23 +01:00
train	New last/train module to train alignment parameters. (#492)	2021-05-19 08:37:08 +01:00