Merged pull requests:
- Update README #107 (ssjunnebo)
- add fix for RT642286 and update tests #106 (vaofford)
- Add --prefix-with-library-name to pf data #105 (vaofford)
- pf supplementary #104 (vaofford)
- Rt635214 bugfixes #103 (vaofford)
- RT635214 bugfixes #102 (vaofford)
- Rt635214 bugfixes #101 (vaofford)
- replace spaces with underscores in stats filenames #100 (vaofford)
- update filename in summary to be same as filename when symlinked with -l #99 (vaofford)
- Add summary to pf rnaseq #98 (vaofford)
- fix mapfind warnings in RT60081 #97 (vaofford)
- annotationfind symlink prefix RT629101 #96 (vaofford)
- add canu 1.6 pacbio assembly #95 (andrewjpage)
- Allow for latest MooseX::App #94 (andrewjpage)
- Rnaseq reference extended data #93 (andrewjpage)
- Assembly file error #92 (andrewjpage)
- add lane id to warning message #91 (ssjunnebo)
- remove h5 files from search as they no longer exist #90 (andrewjpage)
- clarify pseudogenome warnings #89 (ssjunnebo)
- PacBio index files #88 (andrewjpage)
- Pacbio bam files #87 (andrewjpage)
- allow for HGAP4.0 results #86 (andrewjpage)
- 598733 qc level option #85 (ssjunnebo)
- lookup file name instead of hierarchy_name #84 (andrewjpage)
- Snp sorted #83 (andrewjpage)
- Large tar file support #82 (andrewjpage)
- rename license file #81 (ssjunnebo)
- update AUTHORS and add LICENSE #80 (ssjunnebo)
- Snp storage path #79 (andrewjpage)
- set NA if sequencescape doesnt have a row #78 (andrewjpage)
- Allow for low memory archive creation #77 (andrewjpage)
- Annotatation stats out of order #76 (andrewjpage)
- Pacbio assembly symlink #75 (andrewjpage)
- lookup all identifiers at once rather than one by one #74 (andrewjpage)
- dont count the results, it triggers more sql queries #73 (andrewjpage)
- filter mappings by input reference #72 (andrewjpage)
- symlink bams and index files #71 (andrewjpage)
- 6 rename kraken file names symlink #70 (andrewjpage)
- 12 snpfind not returning data #69 (andrewjpage)
v0.12 (2017-02-02)
Merged pull requests:
- check if depth_sd is defined #68 (andrewjpage)
- infgen #67 (andrewjpage)
- update to 118 #66 (andrewjpage)
- 7 filter by assembly in annotationfind #65 (andrewjpage)
- use file modification date rather than database date for extended inf… #64 (andrewjpage)
- 10 pf data fastq names #63 (andrewjpage)
- het snp report moved into qc-sample directory #62 (martinghunt)
- Add Docker and repair tests #61 (andrewjpage)
- Check if directories exist before using #59 (andrewjpage)
- suppress warnings with status files #58 (andrewjpage)
- update citation #57 (andrewjpage)
- check number of results returned #56 (andrewjpage)
- Assembly help text #55 (andrewjpage)
v0.11-alpha (2016-04-11)
Merged pull requests:
v0.10-alpha (2016-04-05)
Merged pull requests:
v0.9-alpha (2016-04-05)
Merged pull requests:
v0.8.4-alpha (2016-04-01)
Merged pull requests:
v0.8.3-alpha (2016-03-29)
Merged pull requests:
v0.8.2-alpha (2016-03-29)
Merged pull requests:
v0.8.1-alpha (2016-03-24)
Merged pull requests:
- Convert filenames to Path::Class::File objects #48 (jgtate)
- Fix bug with the "--file_id_type" option for some commands #47 (jgtate)
- Fix naming of files in archives #46 (jgtate)
v0.8-alpha (2016-03-22)
Merged pull requests:
- Fix failing tests for the "qc" command #45 (jgtate)
- Add "map" command #44 (jgtate)
- Fix stats #43 (jgtate)
- Add "reference-names" option to ref command #42 (jgtate)
v0.7-alpha (2016-03-11)
Merged pull requests:
- Fix assembly bug #40 (jgtate)
- Add QC command #39 (jgtate)
- Add docs for "--ignore-processed-flag" option #38 (jgtate)
- Add "processed" filtering to commands that need it #37 (jgtate)
v0.6-alpha (2016-03-07)
Merged pull requests:
v0.5-alpha (2016-02-23)
Merged pull requests:
v0.4-alpha (2016-02-22)
Merged pull requests:
v0.3-alpha (2016-02-16)
Merged pull requests:
- Add annotationfind #32 (jgtate)
- Tidy permissions handling #31 (jgtate)
- Make the config a singleton #30 (jgtate)
- Convert Roles to classes #29 (jgtate)
v0.2-alpha (2016-02-02)
Merged pull requests:
- Add "pf assembly" #28 (jgtate)
- Add mechanism to force overwriting of existing files #27 (jgtate)
- Refactor stats tests #26 (jgtate)
- Fix lane role #25 (jgtate)
- Refactor progress bar into a Role #24 (jgtate)
- Change behaviour of "-z" option on "pf data" #23 (jgtate)
v0.1-alpha (2016-01-21)
Merged pull requests:
- Remove manual prereq; not needed after all #22 (jgtate)
- Fix deployment #21 (jgtate)
- Use env vars #20 (jgtate)
- Add accessionfind #18 (jgtate)
- Add travis #17 (jgtate)
- Change to git-style single app and multiple sub-commands #16 (jgtate)
- Multiple schemas #15 (jgtate)
- Ui tweaks #14 (jgtate)
with-separate-apps (2016-01-04)
Merged pull requests:
- Fix test links #13 (jgtate)
- Fix progress bars for gzipping and tar writing #12 (jgtate)
- Log errors too #11 (jgtate)
- Refactor/rename a couple of classes #10 (jgtate)
- Make sure archive filename is a Path::Class::File #9 (jgtate)
- Change progress bar #8 (jgtate)
- Add switch #7 (jgtate)
- Fix exception handling #6 (jgtate)
- Add stats #5 (jgtate)
- Add archiving #4 (jgtate)
- Add symlinking #3 (jgtate)
- Refactor as app #2 (jgtate)
with-multiple-test-dbs (2015-11-16)
Merged pull requests: