added -B/-E to trimfq for keeping first/last INT bp and also -s for shortest read #91
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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
This was referenced Feb 7, 2019
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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 in ractice is used a lot. Regarding popularity of such trimming, one has that, for example: