Bam processing (WIP) - #19

Open

averagehat wants to merge 45 commits into

devfrom

Commits on Feb 10, 2016

added tagreads (tags all reads, doesn't skip any)
averagehat
committed
6c66ad1

Commits on Feb 11, 2016

added tagreads
averagehat
committed
ed0ac2b
tag_bam now sorts and indexes afterwards
averagehat
committed
4aa14ca
added freebayes.jip
averagehat
committed
4d46b24
tagreads now writes to separate file or stdout
averagehat
committed
4c99339
foo
averagehat
committed
6244e29
fixing freebayes
averagehat
committed
eb79428
added bioframes dependency from git url
averagehat
committed
44fbf74
added jip consensus
averagehat
committed
2d7c592
Merge branch 'dev' of https://github.com/VDBWRAIR/bioframework into bam-processing
averagehat
committed
0a7976b

Commits on Feb 12, 2016

added new implementation of consensus
averagehat
committed
e21e14d

Commits on Feb 22, 2016

update
averagehat
committed
44be3d0

Commits on Feb 23, 2016

consensus now handles multiple alts
averagehat
committed
549a244

Commits on Feb 24, 2016

various fixes
Panciera
committed
aefe452
refactoring to simplify and remove deprecated funcs
Panciera
committed
e36a4c1

Commits on Feb 27, 2016

added tests,refactored vcf dict flattening
Panciera
committed
46f2df9

Commits on Mar 2, 2016

add missing dependencies
Panciera
committed
1894e0a
fixed ordering bug
Panciera
committed
4633cc6
fixed groupby bug
Panciera
committed
05b04e8
fixed make_consensus
Panciera
committed
8eb0c38
more tests
Panciera
committed
8e3062c
add failing test
Panciera
committed
33d7db7

Commits on Mar 3, 2016

fixed git+ protocol of biotest dep.
averagehat
committed
d3bfe63
fixed contracts to actual pypy name
averagehat
committed
2faecbf
10/10 working
averagehat
committed
613e825

Commits on Mar 4, 2016

baic types and examples
averagehat
committed
0de7577
typechecking works.
averagehat
committed
bf1b67b
added readme for types
averagehat
committed
c2aecb8
fixed tests, now passing
averagehat
committed
c09b94b
removing old types-hypothesis generator file
averagehat
committed
6a0bd96
added missing typing requirement
averagehat
committed
6cbd2e1
missing deps.
averagehat
committed
4427de8
add typing module dep.
Panciera
committed
50cf3c9
Merge branch 'bam-processing' of https://github.com/VDBWRAIR/bioframework into bam-processing
Panciera
committed
59e18a6
fix failing test
Panciera
committed
23afece
add support for trimming reference
Panciera
committed
bb7f937
fix readme formatting
averagehat
committed
272a115
Merge pull request #21 from VDBWRAIR/types
averagehat
committed
875e1aa

Commits on Mar 22, 2016

Merge branch 'bam-processing' of https://github.com/VDBWRAIR/bioframework into bam-processing
Panciera
committed
a08ab6c
fix VCFRow instantiation
Panciera
committed
bbd8af8

Commits on Mar 23, 2016

more info in consensus's stuff
Panciera
committed
c556a76
add doc for low-depth handling
Panciera
committed
e770b20
restore lowdepth->N so tests can maybe pass
Panciera
committed
c77a809
fixed duplcate args error
Panciera
committed
101f5aa

Commits on Apr 17, 2017

ignroe
Panciera
committed
9795897