04b7f2fc6a
Color scheme consistency. Eliminate density plots that really have no meaning
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(mean target coverage, bad cycles).
2011-07-14 15:16:19 -04:00
1f9a730587
Adding density plots to all the existing simple scatter plots.
2011-07-14 14:29:06 -04:00
2d95c71a1c
Integrate mean/sigma markers into generic plotting functions.
2011-07-14 13:49:27 -04:00
2e45f2fb61
Cleanup -- get a lot of the common plotting operations into functions.
2011-07-14 13:13:15 -04:00
0f568b50fb
Curating the dataset based on 2*sigma filtering, 6 month timestamp.
2011-07-14 09:51:54 -04:00
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
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
7159b14e76
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-01 10:53:49 -04:00
bf29ca21cd
Some bugfixes for yesterday's sparse data population enhancements.
2011-07-01 10:53:07 -04:00
bf3cd1ee72
Merged bug fix from Stable into Unstable
2011-06-30 18:30:22 -04:00
4b17f34640
Fixes to the packaging system to work with the new directory structure.
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Also added a few R scripts to the list of files to include in the resources
directory of the binary distribution, at Ryan's request.
2011-06-30 18:27:17 -04:00
91f8ab115d
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-06-30 18:15:53 -04:00
419bf259ee
Large number of bugfixes for bugs encountered while trying to scale up preQC database generation to all reprocessed data:
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- Better support for missing data, esp. in eval files.
- More R-compatible date formatting.
- Some of the AlignmentSummaryMetrics were only for first of pair.
- Some of the InsertSizeMetrics retrieved data for only one pairing orientation.
- More/better command-line customization.
2011-06-30 18:03:59 -04:00
510efa3313
Merged bug fix from Stable into Unstable
2011-06-30 15:27:04 -04:00
5786b51bcf
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-06-30 15:26:28 -04:00
761347b8d5
The VariantContext utility method used by SelectVariants wasn't checking the filter status (unfiltered vs. passing filters) and always returned a VC that was passing filters. This is fixed and the md5 from the VCF Streaming test has been re-updated.
2011-06-30 15:26:09 -04:00
47b47078ad
Merged bug fix from Stable into Unstable
2011-06-30 15:22:14 -04:00
64048a67e8
cleaning up ghost scala scripts. Deleting clearly unused one and moving others to qscripts.archive
2011-06-30 15:20:43 -04:00
b17ed7e504
Merged bug fix from Stable into Unstable
2011-06-30 15:04:30 -04:00
867056af51
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-06-30 15:03:18 -04:00
57806d514a
Merged bug fix from Stable into Unstable
2011-06-30 15:01:50 -04:00
defa3cfe85
Moved around private walkers into appropriate directories in private gatk.walkers. Moved a few public walkers into private qc package, and some private qc walkers into the public directory. Removed several obviously broken and/or unused walkers.
2011-06-30 14:59:58 -04:00
75f93882c7
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-06-30 14:59:10 -04:00
41c43d6248
Merged bug fix from Stable into Unstable
2011-06-30 14:56:42 -04:00
2cb1376ed0
VCFStreaming was failing integration tests because now select variants outputs the samples in alphabetical order, instead of random as before. Fixed the MD5.
2011-06-30 14:55:39 -04:00
f4ae6edb92
Moving some of the released R scripts into public from private
2011-06-30 14:55:25 -04:00
197b7141c1
Added an optional argument -bt <num_threads> for BWA to run multithreaded.
2011-06-30 14:41:57 -04:00
f4463d38ca
BWA requires pair ended reads to be sorted by read names when operating over BAM files, but Picard sorts by coordinate, so in case we use BWA in pair ended reads, the pipeline now resorts the BAM in read name order, realigns it then sorts it in coordinate order.
2011-06-30 14:29:21 -04:00
5d112219e7
Merged bug fix from Stable into Unstable
2011-06-30 13:50:51 -04:00
bb6b1d615b
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-06-30 13:50:16 -04:00
26c4ef3813
Merged bug fix from Stable into Unstable
2011-06-30 13:18:44 -04:00
804d5f22d5
Reverting previous change, as promised.
2011-06-30 13:18:30 -04:00
521a0710e3
Merged bug fix from Stable into Unstable
2011-06-30 13:17:29 -04:00
9e234cf5d6
This is a temporary commit for Picard. It will absolutely break integration tests, but I'm going to revert it in 1 minute. Because we don't want them in unstable, I need to push this into stable.
2011-06-30 13:17:14 -04:00
8a5bfb425c
Merged bug fix from Stable into Unstable
2011-06-30 11:56:14 -04:00
352c38fc0b
Updated to reflect dbsnp conversion fix
2011-06-30 11:55:56 -04:00
58720601b4
Merged bug fix from Stable into Unstable
2011-06-30 11:44:33 -04:00
f51478595b
I guess I don't want to lose these
2011-06-30 11:43:46 -04:00
efd99c3c11
new home for the core qscripts
2011-06-30 11:32:06 -04:00
a26a793532
moving the oneoffs queue scripts to their new home.
2011-06-30 11:29:33 -04:00
843f604be2
Bugfixing: better handling of missing Picard directories. Writing dates in
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a format more conducive to R parsing.
2011-06-30 11:20:50 -04:00
7cfe9d1f94
Merged bug fix from Stable into Unstable
2011-06-30 01:17:32 -04:00
36620c62be
Saving the walkers I 'care about'.
2011-06-30 00:20:26 -04:00
6382232279
Opting to maintain the Replication/Validation files/package in unstable/private. Resolving the conflict from the stable -> unstable merge so it doesn't affect other mergers in the futures.
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Conflicts:
private/java/src/org/broadinstitute/sting/gatk/walkers/replication_validation/ReplicationValidationWalker.java
2011-06-29 18:30:46 -04:00
a3c17a38bb
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-06-29 18:26:11 -04:00
0d1978756e
Removing the replication/validation files and package from the stable repo. It should only exist in private/unstable.
2011-06-29 18:25:47 -04:00
9e5d0d8155
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-06-29 18:09:58 -04:00
231845ab2f
Moved around packages and imports for the Replication Validation walker to work with the new private/public framework.
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Pooled caller implemented but is failing tests (always choosing AC=0).
2011-06-29 18:09:26 -04:00
ef51429b66
Merged bug fix from Stable into Unstable
2011-06-29 17:38:00 -04:00
f18fffd625
Fixing broken paths to the testdata directory throughout the codebase.
2011-06-29 17:36:47 -04:00
Matt Hanna
David Roazen
Eric Banks
Mauricio Carneiro
Mark A. DePristo
Ryan Poplin