b2ade16deb
More detail in pre-QC plots, plus much improved handling of samples with
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special characters in the name.
2011-07-12 11:43:03 -04:00
05212aea62
reader now takes an argument for the maximum number of elements to read from the file.
2011-07-12 08:53:19 -04:00
8056a3fe89
getElement() now uses O(1) get from hash instead of linear O(n) search. Enables us to read large files easily.
2011-07-12 08:52:31 -04:00
f313e14e4e
Now deletes the dump directory on ant clean
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Moving diffengine tests from private to public
2011-07-12 08:50:58 -04:00
b0127f6578
Merge branch 'laptop'
2011-07-12 01:32:16 -04:00
23f2c5fabc
Fixed a bug where the first variant in a haplotype was not getting phased properly.
2011-07-12 01:31:58 -04:00
d7d15019dd
Adding support for other simple header line types (e.g. ALT) and cleaning up the interface a bit.
2011-07-12 01:16:21 -04:00
89792ee0f7
Prototype for incorporating RBP information into trio-phased data
2011-07-12 00:03:12 -04:00
400b0d4422
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-11 23:38:57 -04:00
d5056ad899
Merge branch 'master' into diffit
2011-07-11 23:16:15 -04:00
893cc2e103
Making the package public, so there's no dependances from public -> private
2011-07-11 23:15:08 -04:00
5e593793af
DiffEngine utility function simpleDiffFiles
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printSummaryReport now uses GATKReport for nice formating
Moved print formatting arguments into inner class provided to printing functions themselves, not the class
BAMDiffableReader only reads 1000 entries to avoid performance issue. Work around for BAM files with non-unique names
Uncommented all of the incorrectly commented out CombineVariants integrationtests
BaseTest now uses DiffEngine to provide inline differences to VCF and BAM files
2011-07-11 23:10:27 -04:00
39bd90a8e3
Merge branch 'laptop'
2011-07-11 22:46:35 -04:00
7d579a5b95
PhaseByTransmission now sort the samples in the VCF
2011-07-11 22:45:57 -04:00
6368d5bfad
Attempting to resolve changes to ComputeSwitchErrorRate
2011-07-11 20:53:36 -04:00
e0c03c2c06
Fixed imports
2011-07-11 20:48:17 -04:00
48e5078497
Restored ComputeSwitchErrorRate.java from old SVN repo
2011-07-11 20:40:26 -04:00
2d12976254
Restored ComputeSwitchErrorRate from old SVN repo
2011-07-11 19:44:15 -04:00
d11155ce2e
Merge branch 'master' of ssh://gsa3.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-11 19:19:54 -04:00
e93052a51e
When generating the QGraph, don't regenerate if there aren't scatter/gather jobs.
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Fixed a display issue with the number of milliseconds that Queue has tried to contact LSF.
2011-07-11 19:17:58 -04:00
e3748675db
Support for VCF 4.1 header counts
2011-07-11 17:40:45 -04:00
7a89275458
Count the number of phase error, phase correct, and total phaseable sites
2011-07-11 17:25:02 -04:00
f5a1d8a40f
Count the number of phase error, phase correct, and total phaseable sites
2011-07-11 17:19:40 -04:00
f54c2ae3b4
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-11 16:26:27 -04:00
d6517adb42
Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-11 16:16:37 -04:00
86890c6357
N and K (in binomial probability) got switched in RFA Walker with the last commit. No longer will NaNs be produced.
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Added: TableToVCF. Kind of a longer-term project, but there are lots of variant calls available in a weird tabular format. I used this to convert Ju Et Al small indels to VCF. I'll check against the 1000G ASN superpopulation calls to see if we see a good amount of recapitulation, and if so, i'll put them in unvalidated comparisons. Minor chances to the TableCodec and TableFeatures to allow for this (the codec can sometimes drop a column, and the feature now allows you to grab on to its header).
2011-07-11 16:16:15 -04:00
6ada358f75
Refined some code to print out sites where the haplotypes between RBP and PbT don't match.
2011-07-11 16:11:32 -04:00
7c387eaa47
Refined some code to print out sites where the haplotypes between RBP and PbT don't match.
2011-07-11 16:08:33 -04:00
c04ffc57f2
Added some code to print out sites where the haplotypes between RBP and PbT don't match.
2011-07-11 16:01:50 -04:00
b327fa3779
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-11 15:20:45 -04:00
41db509a17
A simple python program for downloading S3 logs in the cron script.
2011-07-11 15:20:01 -04:00
d587856f2d
Private feature to input a list of family descriptions from a file and to look for MV's on all of these. Feature can also output a detailed description of the violation into a separate file
2011-07-11 14:17:59 -04:00
a18380ab96
Merged bug fix from Stable into Unstable
2011-07-11 12:16:50 -04:00
8a78414432
Removed TileCovariate as a dependency for AnalyzeCovariates.jar
2011-07-11 12:10:11 -04:00
42583ee787
Incorporates information from RBP so that triple hets and sites with missing information can still be phased.
2011-07-11 11:55:28 -04:00
ef17e5db32
Reports the read length distribution for each sample.
2011-07-10 18:56:21 -04:00
feef50802c
Formatting change
2011-07-10 18:29:39 -04:00
125b488a0c
Reports the insert size distribution for each sample.
2011-07-10 18:15:17 -04:00
a6170c522c
Merge branch 'master' of ssh://kiran@nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-10 11:25:37 -04:00
6e7b5e1e7a
Merged bug fix from Stable into Unstable
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Merge branch 'master' into unstable
2011-07-08 21:19:45 -04:00
7fbc5987d0
Merge branch 'master' of ssh://delangel@nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-07-08 21:17:32 -04:00
885ec58093
Overhaul of the PreQC plots, with more distinct separation of current dataset
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vs. historical data.
2011-07-08 17:24:26 -04:00
68e19edf59
Merged bug fix from Stable into Unstable, and resolved merge conflicts.
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Conflicts:
build.xml
settings/ivysettings.xml
2011-07-08 15:50:31 -04:00
a3c9d9c3ff
Fixing Contracts for Java, and enabling contracts by default for unit/integration tests.
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The NullPointerException we were seeing when trying to run with contracts enabled was being caused
by an outdated version of the asm library.
To run tests without contracts and disable their compilation, pass in "-Duse.contracts=false" to ant.
Also did some minor unrelated cleanup in build.xml
2011-07-08 15:34:39 -04:00
bd29236684
Merge branch 'master' into diffengine
2011-07-08 14:08:17 -04:00
8de82f3974
Updated names to be more reflective of the fact that this works for exomes and WG now.
2011-07-08 14:07:28 -04:00
ae02eabc93
Since it now works with all classes of variants, should really be renamed
2011-07-08 14:04:59 -04:00
2ea36b06cc
Really works now with files where (1) there's no functional annotation and (2) there's no indel calls.
2011-07-08 14:04:00 -04:00
38d9b9b568
A printf from debugging made it in in some prior commit.
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The read transform adding the AI tag can cause an exception for widowed reads -- added a check for this case, preventing blowup.
2011-07-08 13:13:58 -04:00
51338cbe07
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-08 12:49:00 -04:00
Matt Hanna
Mark DePristo
Kiran V Garimella
Eric Banks
Khalid Shakir
Guillermo del Angel
Christopher Hartl
David Roazen
Ryan Poplin