Change Log
Unreleased
Merged pull requests:
v1.4.1 (2018-09-20)
Merged pull requests:
1.4.1 (2018-07-19)
Closed issues:
Merged pull requests:
- Change TryCatch to Try::Tiny #94 (ssjunnebo)
- fix typo in badge #93 (ssjunnebo)
- Include TOC #92 (ssjunnebo)
- 621538 docker #91 (ssjunnebo)
- 621538 docker #90 (ssjunnebo)
- include reference genome for cram #89 (ssjunnebo)
- Revert "Replace cram file without reads" #88 (ssjunnebo)
- Replace cram file without reads #87 (ssjunnebo)
- update tutorial for ENA switch to https (from http) #85 (lbarquist)
1.4.0 (2017-11-28)
Closed issues:
Merged pull requests:
- include last base of annotation in insertion count #82 (lbarquist)
- Rename license file' #79 (ssjunnebo)
- update AUTHORS and rename LICENSE #78 (ssjunnebo)
- Tmp file time stamp #77 (ssjunnebo)
v1.3.3 (2017-05-08)
Merged pull requests:
v1.3.2 (2017-05-08)
Closed issues:
Merged pull requests:
- modified ranges to accommodate higher density insertion data #74 (lbarquist)
- removed File::Slurp #73 (vaofford)
- dont add POD to R scripts #72 (andrewjpage)
v1.3.1 (2016-09-23)
Closed issues:
- Mapping score always set to 1 if -m option used with plot_tradis #66
- Error in step 3.5 of bacteria_tradis, using samtools 1.3 #63
Merged pull requests:
- change to dist zilla starter bundle #70 (nds)
- switch PCR primers #69 (andrewjpage)
- updated readme #68 (lbarquist)
- Fix for bug #66, change mapping_score option spec in B::T::CL::PlotTradis #67 (RoyChaudhuri)
v1.3.0 (2016-04-13)
Merged pull requests:
- Merge Roys changes #65 (andrewjpage)
- added recipes (again) #62 (lbarquist)
v1.2.4 (2015-12-11)
Closed issues:
- tradis_essentiality.R #28
Merged pull requests:
v1.2.3 (2015-11-03)
Merged pull requests:
- Bump the version number #59 (bewt85)
- Ticket 463867: What if a tag isn't found? #58 (bewt85)
- updated bacteria_tradis help messages #57 (lbarquist)
- Add package version module to dist zilla #56 (andrewjpage)
v1.2.2 (2015-09-14)
Merged pull requests:
- Added sequencing recipes #55 (lbarquist)
- updated help messages for R scripts #54 (lbarquist)
- POD formatting #53 (andrewjpage)
v1.2.1 (2015-09-10)
Merged pull requests:
- Simplify installation #52 (andrewjpage)
v1.2 (2015-09-08)
Merged pull requests:
- Ticket 473325: Install two different versions of SAMTOOLS #51 (bewt85)
- Add TravisCI support #50 (bewt85)
- fixed filtering bug #49 (lbarquist)
- Updated shebang line in R scripts for portability #48 (carlacummins)
- added installation notes #47 (lbarquist)
- only require 2 command line args, not 3 #46 (lbarquist)
- Bug fixes and added features #45 (carlacummins)
- Adding tabix a prerequisite #44 (js21)
- Cram file output #43 (andrewjpage)
- Code is now cross-platform #42 (js21)
- Pass through samtools exec and verbose mode #41 (andrewjpage)
- Cram support #40 (andrewjpage)
- added the missing test files #39 (js21)
- suppressed uninitialised warnings when importing PE data #38 (carlacummins)
- Tabix indexed plot files in place #37 (js21)
- added filtering option, so default is old behavior. -f now enables read ... #36 (lbarquist)
- fixed typo #35 (lbarquist)
- feature addition to tradis_comparison, bugfix tradis_essentiality #34 (lbarquist)
- Added AUTHORS file #33 (aslett1)
- Fixed problem with opening combined plots in Artemis #32 (carlacummins)
- Fixed problem with unusual characters in filenames #31 (carlacummins)
- Updates #30 (carlacummins)
- index needs to be offset by 2 #29 (raeece)
- Fixed issue with exposed -y smalt param #27 (carlacummins)
- Exposed -y smalt parameter #26 (carlacummins)
- Added GPL-LICENCE #25 (carlacummins)
- Fixed problems with merging plots #24 (carlacummins)
- Updates to help text #23 (carlacummins)
- Added R scripts #22 (carlacummins)
- Removed leftover debugging statement #21 (carlacummins)
- Exposed SMALT indexing parameters #20 (carlacummins)
- Bug fix #19 (carlacummins)
- Fix for combined plots not reading in Artemis #18 (carlacummins)
- gzip no prompt for overwrite #17 (carlacummins)
- Fixed problem with blank lines #16 (carlacummins)
- Fixed combine_tradis_plots #15 (carlacummins)
- Plot update #14 (carlacummins)
- Updated help text for combine_tradis_plots #13 (carlacummins)
- Added module to combine plot files #12 (carlacummins)
- Further file checking updates #11 (carlacummins)
- Bug fix in file existance check #10 (carlacummins)
- Updates #9 (carlacummins)
- Updated bacteria_tradis help #8 (carlacummins)
- Distribution ready #7 (carlacummins)
v1.132190 (2013-08-07)
v1.132140 (2013-08-02)
Merged pull requests:
- Complete package v1 #6 (carlacummins)
- fix cigar string #5 (andrewjpage)
- Reverse complement fix #4 (andrewjpage)
- die if the number of reads outputted differs #3 (andrewjpage)
- Executables in bin #2 (carlacummins)
- Bio-Tradis #1 (carlacummins)