najoshi/sickle issues and pull requests

#59 - Correct command question for trimming to a fixed length

Issue - State: open - Opened by t221f over 1 year ago

#58 - sickle not found though installed.

Issue - State: open - Opened by skr3178 about 2 years ago

#57 - WARNING: PE file 2 is shorter than PE file 1

Issue - State: open - Opened by vappiah almost 4 years ago

#56 - Using -g increases runtime

Issue - State: open - Opened by PelFritz almost 4 years ago

#55 - questions about filtering out reads based on the first 3 bases quality in reads before adaptor trimming

Issue - State: open - Opened by santataRU over 4 years ago

#54 - Not an issue but questions

Issue - State: open - Opened by FritzPeleke over 4 years ago - 2 comments

#53 - No annotation for the options

Issue - State: open - Opened by MiltonKoB about 6 years ago

#52 - "Segmentation fault (core dumped)" depending on parameters naming

Issue - State: open - Opened by rioualen over 7 years ago - 2 comments

#51 - Fix off-by-one error finding 3' cutoff.

Pull Request - State: open - Opened by MikkelSchubert over 7 years ago

#50 - bioconda

Issue - State: open - Opened by dridk almost 8 years ago - 2 comments

#49 - sickle pe makes unpaired output

Issue - State: closed - Opened by dcopetti over 8 years ago - 5 comments

#48 - Develop

Pull Request - State: closed - Opened by dstreett over 8 years ago

#47 - Quality Scores in illumina reads too low

Issue - State: open - Opened by tobsecret almost 9 years ago - 2 comments

#46 - Citable DOI for repository via Zenodo

Issue - State: open - Opened by jdblischak about 9 years ago

#45 - Tabs

Pull Request - State: closed - Opened by dstreett about 9 years ago

#44 - Rework Galaxy wrapper.

Pull Request - State: open - Opened by nsoranzo about 9 years ago - 1 comment

#43 - Use stderr for all logging messages

Pull Request - State: open - Opened by kdm9 over 9 years ago - 2 comments

#42 - Can't chose window size

Issue - State: open - Opened by xapple over 9 years ago - 1 comment

#41 - [4/4] -n / -N options: Only consider Ns between the sliding window cut sites (+ tests!)

Pull Request - State: open - Opened by tsibley almost 10 years ago

#40 - [1/4] Option sync and usage cleanup

Pull Request - State: open - Opened by tsibley almost 10 years ago

#39 - -n / -N options: Only consider Ns between the sliding window cut sites

Pull Request - State: closed - Opened by tsibley about 10 years ago - 1 comment

#38 - Orphan quality and length thresholds

Pull Request - State: open - Opened by jdidion about 10 years ago

#37 - Different quality and length thresholds for paired-end and single-end reads

Issue - State: open - Opened by jdidion about 10 years ago

#36 - [3/4] Optionally use a fixed window size instead of 0.1 of the read length

Pull Request - State: open - Opened by tsibley about 10 years ago - 4 comments

#35 - [2/4] Add a --drop-n / -N option to drop any sequence containing an N

Pull Request - State: open - Opened by tsibley over 10 years ago - 1 comment

#34 - Option segfault and usage cleanup

Pull Request - State: closed - Opened by tsibley over 10 years ago - 1 comment

#33 - testing / fixing issue 32

Pull Request - State: open - Opened by wookietreiber over 10 years ago - 1 comment

#32 - segfault on empty reads

Issue - State: open - Opened by roryk over 10 years ago - 10 comments

#31 - standard build using GNU autotools

Pull Request - State: open - Opened by wookietreiber over 10 years ago - 2 comments

#30 - Change behavior of -n option

Issue - State: closed - Opened by monicabritton over 10 years ago - 1 comment

#29 - pull request for version 1.31

Pull Request - State: closed - Opened by ucdavis-bioinformatics over 10 years ago

#28 - [WIP] implement a CLI option to output singles to same file as interleaved output

Pull Request - State: closed - Opened by kdm9 over 10 years ago - 5 comments

#27 - Tuned sliding.c and added support for colorspace

Pull Request - State: closed - Opened by biocyberman over 10 years ago - 1 comment

#26 - Merge pull request

Pull Request - State: closed - Opened by ucdavis-bioinformatics over 10 years ago

#25 - Merge pull request #3 from najoshi/master

Pull Request - State: closed - Opened by ucdavis-bioinformatics over 10 years ago

#24 - differerence in number of kept reads between with and without 5' trimming?

Issue - State: open - Opened by biocyberman over 10 years ago - 2 comments

#23 - Trimming colorspace reads

Issue - State: open - Opened by biocyberman over 10 years ago - 1 comment

#22 - Citation

Issue - State: closed - Opened by pedrocrisp over 10 years ago - 1 comment

#21 - sickle_singletons_file

Issue - State: closed - Opened by cdmarsden about 11 years ago

#20 - problem with length threshold

Issue - State: closed - Opened by boryanakis about 11 years ago - 4 comments

#19 - pull request

Pull Request - State: closed - Opened by ucdavis-bioinformatics over 11 years ago

#18 - pull request

Pull Request - State: closed - Opened by ucdavis-bioinformatics over 11 years ago

#17 - pull request

Pull Request - State: closed - Opened by ucdavis-bioinformatics over 11 years ago

#16 - Concerning libz

Issue - State: closed - Opened by nkav over 11 years ago - 4 comments

#15 - Fix linker error: undefined reference to `gzread'

Pull Request - State: closed - Opened by sjackman over 11 years ago - 1 comment

#14 - Fixes quality encoding for phred33 scores

Pull Request - State: closed - Opened by gedankenstuecke over 11 years ago - 1 comment

#13 - phred33 quality scores

Issue - State: closed - Opened by fgvieira over 11 years ago - 6 comments

#12 - Citation

Issue - State: closed - Opened by audy almost 12 years ago - 2 comments

#11 - Please add a git-tag for release versions, so homebrew can use that

Issue - State: closed - Opened by samueljohn almost 12 years ago - 2 comments

#10 - makefile

Issue - State: closed - Opened by nsaarman about 12 years ago - 5 comments

#9 - 5' Trimming Bug

Issue - State: closed - Opened by nathanhaigh about 12 years ago - 1 comment

#8 - fixed lengths

Issue - State: closed - Opened by wbsimey over 12 years ago

#7 - Disable 5'-trimming and enable removal of sequences with Ns - Not working

Issue - State: closed - Opened by a1aks over 12 years ago - 1 comment

#6 - altered to work with combined paired-end input files

Pull Request - State: closed - Opened by bcthomas over 12 years ago - 2 comments

#5 - Possibility of trimming based on adapter sequences?

Issue - State: closed - Opened by seandavi over 12 years ago - 2 comments

#4 - length restrictions are not enforced

Issue - State: closed - Opened by wwhsiao almost 13 years ago - 4 comments

#3 - trimming on colorspace fastq gives bad output.

Issue - State: closed - Opened by brentp almost 13 years ago

#2 - typo in output

Issue - State: closed - Opened by ngcrawford over 13 years ago

#1 - my changes

Pull Request - State: closed - Opened by vsbuffalo almost 14 years ago - 1 comment

GitHub / najoshi/sickle issues and pull requests