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Merged
merged 42 commits into from
Jun 10, 2015
Merged

Version 4.2.2 #54

merged 42 commits into from
Jun 10, 2015

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@pimentel
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  • pseudobam
  • threaded bootstrap

pmelsted and others added 30 commits May 20, 2015 15:18
@pmelsted
Bias, counts hexamers now
5ee180d
@pmelsted
Messes with the index
a00db1f
@pmelsted
Fixes kmerindex, adds orientation
b649393
@pmelsted
Adds info for second pair
a309884
@pmelsted
First pass at bias working
7de9088
@pmelsted
Fixes _
03b47d0
@pmelsted
Does not try to do bias, without bias data
1fd5fbc
@lakigigar
Fixed output typo
04fb059
@pmelsted
Small fixes
4b80944
@pmelsted
Speedups for bias correction
39714f0
@pmelsted
Merge branch 'orient' of https://github.com/pachterlab/kallisto into …
51c559c 
…orient
@pimentel
Merge pull request #49 from pachterlab/orient
54d481f 
Orient
@pimentel
abundance.txt to abundance.tsv
4cbe76b
@pimentel
basic thread pool. not actually bootstrapping. need to update interface
aa61359
@pimentel
change bootstrap interface to no longer require EM
423aa2d
@pimentel
prettier printing for threaded bootstraps
6c11318
@pmelsted
Pseudobam working, for paired end but not flags
0be5ae9
@pimentel
add warning if num threads > num bootstraps
aa59407
@pimentel
print pretty numbers with commas
aa122c3
@pmelsted
Pseudobam now has single end mode working, all flags are implemented
83dc536
@pmelsted
Refactored positional information, added hanging chads detection
7003d96
@pmelsted
Fixed hanging chad if input length supplied
c78d7a9
@pmelsted
Fixed usage message
7c5faff
@pmelsted
Fixed merge
5cb3102
@pmelsted
Merge branch 'pseudobam' into devel
434053a
@pmelsted
merged devel into prettyprint
081a043
@pmelsted
Merge branch 'hjp/prettyprint' into devel
9f36e8a
@pmelsted
merged devel into threads
e199f3e
@pmelsted
Merge branch 'hjp/threads' into devel
6bbc307
@pimentel
possible fix for linux build
87a5596
pimentel added a commit that referenced this pull request Jun 10, 2015
@pimentel
Merge pull request #54 from pachterlab/devel
0e6701d 
Version 4.2.2
@pimentel pimentel merged commit 0e6701d into master Jun 10, 2015
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3 participants

@pimentel @pmelsted @lakigigar