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Master - #75

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bgistone wants to merge 184 commits into

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master

Open

Master#75
bgistone wants to merge 184 commits into
parallelfrom
master

Commits on Mar 13, 2015
- Update README.md
  cc2qe
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- Update README.md
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- fix verbose stuff
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- update make
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- Merge branch 'install'
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- Update README.md
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- Update README.md
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- Update README.md
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- Update README.md
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- Update README.md
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- Update README.md
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- Update README.md
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- Update README.md
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- Update README.md
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- Update README.md
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- Update README.md
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- Update README.md
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- get rid of new lines
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- Merge branch 'master' of github.com:cc2qe/speedseq
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- add workflow image
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- Update README.md
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- image
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- Merge branch 'master' of github.com:cc2qe/speedseq
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- Update README.md
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- Update README.md
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- automatically index reference with BWA if absent
  EC2 Default User
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- Update README.md
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- init example install
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- Update README.md
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- Update README.md
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Commits on Mar 14, 2015
- example install script
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- Update README.md
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- add python explicit
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- bump lumpy
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- mktemp compatible with mac
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- fix issue #20 https://github.com/cc2qe/speedseq/issues/20
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- add example script
  EC2 Default User
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- organized
  EC2 Default User
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- in case speedseq not in path
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- Update README.md
  cc2qe
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- Update README.md
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- Update README.md
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- rename
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- Merge branch 'master' of github.com:cc2qe/speedseq
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- Update README.md
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- remove svtools submodule
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- bump svtyper
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- make
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- bump lumpy
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- more informative checking for python modules
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- bwa version 0.7.8, in accordance with speedseq paper
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- add screenshots for amazon ami documentation
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- Update README.md
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- Update README.md
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Commits on Mar 15, 2015
- Update README.md
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- Update README.md
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- Revert "Update README.md"
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- Merge branch 'master' into hall
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- update example speedseq.config
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- add hall speedseq config
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- hall lab bwa v.0.7.10
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- add version 0.0.3
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- Merge branch 'master' into hall
  cc2qe
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- better dependency checking
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- Update README.md
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- Update README.md
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- Update README.md
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Commits on Mar 16, 2015
- bump svtyper ms version
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Commits on Mar 19, 2015
- update iwth master
  cc2qe
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- fix svtyper
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Commits on Mar 24, 2015
- Update README.md
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Commits on Mar 25, 2015
- Update README.md
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Commits on Mar 27, 2015
- remove option to only output somatic variants
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Commits on Mar 29, 2015
- Update README.md
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Commits on Apr 1, 2015
- version info
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Commits on Apr 2, 2015
- speedseq realign handles multiple BAM files
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- help menu
  cc2qe
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- clean up
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Commits on Apr 3, 2015
- bump to speedseq vawk which uses gawk (confusing, right?)
  cc2qe
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Commits on Apr 7, 2015
- Merge branch 'multibam' of github.com:cc2qe/speedseq into multibam
  cc2qe
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Commits on Apr 29, 2015
- update sambamba to v0.5.4. also, do not output sequence or qual for splitters and discordants
  EC2 Default User
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Commits on May 1, 2015
- Update README.md
  cc2qe
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Commits on May 14, 2015
- bump svtyper
  cc2qe
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Commits on May 18, 2015
- bump submodules
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- bump submodules
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Commits on Jun 5, 2015
- annoate copy number of BND variants
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Commits on Jun 26, 2015
- bump samblaster to 0.1.22
  cc2qe
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- bump lumpy to handle supplementary flag and bamkit
  cc2qe
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- bump svtyper
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Commits on Jul 3, 2015
- more explicit about pysam versions
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Commits on Aug 3, 2015
- bump freebayes to version v0.9.21
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Commits on Aug 17, 2015
- bump versions for supplementary read support
  cc2qe
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- bump freebayes version
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- Merge branch 'gms'
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- remove hall config from master
  cc2qe
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- merge developmental features to master
  cc2qe
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- Update README.md
  cc2qe
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- Update README.md
  cc2qe
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- Update README.md
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- Update README.md
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- Update README.md
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Commits on Aug 18, 2015
- Corrected CNVnator command echo for verbose output
  s-boardman
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- Merge pull request #39 from s-boardman/master
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Commits on Aug 24, 2015
- hopefully fixed error with empty cigar string related to modifications in pysam 0.8.1 (None instead of [] #30 )
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Commits on Aug 27, 2015
- Update README.md
  cc2qe
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- added license, #43
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Commits on Sep 3, 2015
- add logo
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- svg logo
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Commits on Sep 8, 2015
- bumpy lumpy to address zero-length read, remove element issue
  cc2qe
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  be66448
- Merge branch 'master' of github.com:cc2qe/speedseq
  cc2qe
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Commits on Oct 12, 2015
- Update README.md
  cc2qe
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  c6ae1bc
Commits on Oct 26, 2015
- bump lumpy
  cc2qe
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  c1058b7
Commits on Oct 27, 2015
- if reference index absent, speedseq automatically indexes reference with BWA before realign #49
  cc2qe
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  b3520fa
- allow user-specified window size #38
  cc2qe
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- Merge branch 'cnvnator_windows'
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Commits on Nov 13, 2015
- update prereqs for gawk
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- force bitwise sorting, #53
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Commits on Nov 30, 2015
- address #63 with VEP assembly parameter -a for 'var', 'somatic', and 'sv'
  cc2qe
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- Merge branch 'master' of github.com:cc2qe/speedseq
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- add dino
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- add pipefail
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Commits on Jan 12, 2016
- update sambamba, add realign test
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Commits on Jan 22, 2016
- verbose is now the default
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Commits on Jan 28, 2016
- pipefail caused 147 exit statuses, like in
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Commits on Mar 11, 2016
- bump svtyper
  cc2qe
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  9185e8d
- bump again
  cc2qe
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- bump again
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Commits on Mar 30, 2016
- Update README.md
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Commits on Apr 5, 2016
- bump svtyper
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- Merge branch 'master' of github.com:cc2qe/speedseq
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Commits on May 30, 2016
- realign: auto-generate readgroup info (when input BAMs lack RGs), or allow the user to specify them on command line https://github.com/hall-lab/speedseq/issues/35
  cc2qe
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  b122aba
- fixed a couple bugs related to #35
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Commits on Jun 15, 2016
- Update README.md
  cc2qe
  authored
  6fe658e
Commits on Jun 20, 2016
- fix bug in VEP annotation of non-autosomes #81
  cc2qe
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Commits on Jul 12, 2016
- fix 'no chromosomes found' error in cnvnator, for BAMs with extra header metadata
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Commits on Jul 13, 2016
Commits on Aug 10, 2016
- fix bug in cnvnator header parsing
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Commits on Nov 1, 2016
- Update README
  ahwagner
  authored
  3ab092d
- Merge pull request #93 from ahwagner/patch-1
  cc2qe
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Commits on Nov 2, 2016
- Update Makefile
  cc2qe
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  87b19b6
Commits on Nov 21, 2016
- bump svtyper
  cc2qe
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  9835a76
- Merge branch 'master' of github.com:cc2qe/speedseq
  cc2qe
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  6f93db3
- bump svtyper to v0.1.0
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Commits on Dec 6, 2016
- temporarily rollback svtyper to v0.0.4, to avoid a bug in dup and inversion genotyping
  cc2qe
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Commits on Dec 13, 2016
- bump svtyper to v0.1.1
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Commits on Dec 14, 2016
- FAQ to address #31 and #94
  cc2qe
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Commits on Jan 9, 2017
- bump version tags
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Commits on Mar 7, 2017
- detect CRAM file by extension and add flags for sambamba
  ernfrid
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- + inspect the binary file header to detect CRAM/BAM
  
  indraniel
  authored and
  ernfrid
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- cnvnator wrapper with modification so it doesn't hang on large bam header inputs
  
  apregier
  authored and
  ernfrid
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  63b3c1d
- Simplify cnvnator_wrapper and use deployed version of new cnvnator
  
  apregier
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  ernfrid
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  65cc034
- Exclude alts and decoys
  
  apregier
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  ernfrid
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- Need -t argument for compatibility even though it is not used
  
  apregier
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  ernfrid
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  0ccb472
- Merge in Colbys fix from the main repo to allow arbitrary numbers of fields in the SQ header
  
  apregier
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  ernfrid
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- introduce changes made by idas
  ernfrid
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- remove some dead code
  ernfrid
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- add timestamps, threading, and whitespace fixes
  ernfrid
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  efcdee6
- allow specification of samtools binary
  ernfrid
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  fcbaac1
- make regex exclusion somewhat configurable. Should work alright for human.
  ernfrid
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  ecb338a
- separate wrappers from cnvnator in makefile
  ernfrid
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- abstract hexdump into an environment variable
  ernfrid
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- add hexdump to autogenerated config
  ernfrid
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- remove lumpy submodule
  ernfrid
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- add cram compatible lumpy update
  ernfrid
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Commits on Mar 11, 2017
- use samtools in config and for cnvnator_wrapper
  ernfrid
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- use latest svtyper
  ernfrid
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  032bb7a
Commits on Mar 28, 2017
- Merge pull request #103 from ernfrid/v0.1.2_cram_support
  cc2qe
  authored
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- command line arg for ref FASTA (for CRAM reading)
  cc2qe
  committed
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- Revert "command line arg for ref FASTA (for CRAM reading)"
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Commits on Apr 17, 2017
- bump to svtyper v0.1.3
  cc2qe
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  8190a77
- use official cnvnator
  cc2qe
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  176e463
- add samtools for cnvnator
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  8198ad9
- compilation for official cnvnator
  cc2qe
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- remove samtools submodule
  cc2qe
  committed
  e002f78
- update cnvnator installation instructions
  cc2qe
  authored
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- cnvnator instructions
  cc2qe
  authored
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- update lumpy
  cc2qe
  committed
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- Merge branch 'v0.1.2_cram_support' of github.com:hall-lab/speedseq into v0.1.2_cram_support
  cc2qe
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Commits on Apr 19, 2017
- bump svtyper to 1.4
  cc2qe
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  8814723
Commits on Apr 26, 2017
- revert LUMPY to avoid htslib conflicts with speedseq make (#106)
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Commits on Feb 8, 2018
- Add new exclude files
  apregier
  committed
  bb19df6
- Merge pull request #125 from hall-lab/new_exclude
  apregier
  authored
  4e60002

Commits

Commits on Mar 13, 2015

Commits on Mar 14, 2015

Commits on Mar 15, 2015

Commits on Mar 16, 2015

Commits on Mar 19, 2015

Commits on Mar 24, 2015

Commits on Mar 25, 2015

Commits on Mar 27, 2015

Commits on Mar 29, 2015

Commits on Apr 1, 2015

Commits on Apr 2, 2015

Commits on Apr 3, 2015

Commits on Apr 7, 2015

Commits on Apr 29, 2015

Commits on May 1, 2015

Commits on May 14, 2015

Commits on May 18, 2015

Commits on Jun 5, 2015

Commits on Jun 26, 2015

Commits on Jul 3, 2015

Commits on Aug 3, 2015

Commits on Aug 17, 2015

Commits on Aug 18, 2015

Commits on Aug 24, 2015

Commits on Aug 27, 2015

Commits on Sep 3, 2015

Commits on Sep 8, 2015

Commits on Oct 12, 2015

Commits on Oct 26, 2015

Commits on Oct 27, 2015