added -B/-E to trimfq for keeping first/last INT bp and also -s for shortest read #90
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added -B/-E to trimfq for keeping first/last INT bp"
fixing bugs and also "shortcircuting" the case when param == 0
fixing bugs
fixing description
Updated with -B/-E for trimfq examples
fixed typo "rigth" to "right"
updated version string to 1.0-r68a-dirty
Added the possibility to use simultaneously in trimfq: a) -e with -E, and b) -b with -B.
Added examples for use simultaneously use with trimfq of: a) -e with -E, and b) -b with -B.
setting the minimum length
the minimum reads after the trimming is 1 instead of zero (no reads with length 0 are created)
fixes
fixes bugs and descriptions of "trimfq -l"
Adding example for "trimfq -l" usage with other trimming options.
trying to fix locally the bug where reads with no sequence are converted to FASTA format in TRIMFQ and also setting be default "trimfq -l" to 1 instead of 30.
fixing bug in trimfq
fixed bugs regarding trimfq
updated to the version string to: 1.0-r68e-dirty
4 tasks
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Please make changes on the latest master branch. Thanks. |
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This is basically a resurrected issue #38 which was brought up to date to the latest release of seqtk such that they do not interfere with the original command line options of seqtk anymore.
More precisely this adds for trimfq the following:
This allows a more precise control of how trimming is done. This kind of trimming is used heavily in FusionCatcher (by using a forked seqtk instead of the original seqtk). Here #38 was mentioned that this kind of trimming is rare but actually inp ractice is used a lot. Regarding popularity of such trimming, one has that, for example: