55c8c05060
Merge branch 'master' of ssh://delangel@nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-07 06:18:29 -04:00
5ab2e83904
a) Cosmetic modifications to IndelType annotation. b) Add ability to select samples from a file in PrintReads, c) fixes to shaped AF random selection in SelectVariants
2011-07-07 06:15:10 -04:00
ccf34f7e45
(1) Added very useful helper class TestDataProvider to BaseTest that making creating data providers for TestNG far easier
...
(2) DiffEngine now officially working with with summaries. Extensive UnitTests all around!
2011-07-06 21:57:22 -04:00
52f6f9fdcc
Merged bug fix from Stable into Unstable
2011-07-06 16:05:48 -04:00
54121eb082
Catch malformed bams that cause the writer to run in infinite loops
2011-07-06 16:05:08 -04:00
3ed6d494ce
Huh, guess I forgot to commit this one.
2011-07-06 15:58:12 -04:00
ebf117f1fe
Change packages to reflect current structure. Remove @Overrides on interface methods.
2011-07-06 14:05:50 -04:00
76a01a7453
Merged bug fix from Stable into Unstable
2011-07-06 12:53:09 -04:00
14fee4ccbd
Patch from Bob to deal with symbolic alleles: these weren't getting padded but they should be.
2011-07-06 12:51:44 -04:00
a5ad603b35
Gah. Missed one.
2011-07-06 12:15:41 -04:00
759bc25643
Get rid of the dumb backups
2011-07-06 12:15:04 -04:00
f5890b1715
Moving RFA from string/walkers to sting/gatk/walkers (PSP2 as well). Dumb emacs backups committed accidentally, will be removed shortly.
2011-07-06 12:12:25 -04:00
515553c801
Merged bug fix from Stable into Unstable
2011-07-06 11:34:13 -04:00
0b86958a56
Merge branch 'master' of ssh://gsa3/humgen/gsa-scr1/gsa-engineering/git/stable
2011-07-06 11:33:15 -04:00
c93d0b37a8
Fixed namespace of the pipeline classes.
2011-07-06 11:32:46 -04:00
bdef233d4d
Merged bug fix from Stable into Unstable
2011-07-06 10:05:02 -04:00
e8ed6b7f0f
Adding more comments to main VQSR walker. Fixing copyright lines. Bug fix for default paths to now point to public/R/ instead of R/ Bug fix in VQSR for the path to the R scripts not ending in a slash.
2011-07-06 10:01:14 -04:00
8e8b901d12
Merged bug fix from Stable into Unstable
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Merge branch 'master' into unstable
2011-07-06 09:57:55 -04:00
81a4d18468
Mark several indel-related arguments as @Hidden
2011-07-06 09:56:38 -04:00
1f1231f47a
Implementation of key summarizing algorithm and support routines. UnitTests for support routines. Almost ready to test the summarizer on real difference set.
2011-07-05 23:23:49 -04:00
7b699f8b17
Switched GridEngine from looking from environment variable to using embedded jar.
2011-07-05 21:59:00 -04:00
407a0e535f
Merged bug fix from Stable into Unstable
2011-07-05 16:34:21 -04:00
5298e3a942
Making the outputDir optional. Default = ./
2011-07-05 16:30:41 -04:00
7d3dfdfdf2
Updating the MDCP to use the classpath for the GATK jar, removing -gatk parameter.
2011-07-05 16:30:10 -04:00
080875d5da
Refactored DiffNode/DiffElement/DiffValue class structure. DiffElement is now a pair of Name -> Value, where value is either a DiffValue or its subclass DiffNode. Code cleaned up, more tests added. DiffEngine is now working, with tests. DiffObjectWalker can now take two VCFs and itemize the difference between the two files correctly and concisely.
2011-07-05 16:13:39 -04:00
a765c08381
New home for the ReducedBAMEvaluation qscript.
2011-07-05 13:58:50 -04:00
592e79a4ba
There is no pretty way to do this unfortunately.
...
How to remove files from STABLE, sync with UNSTABLE but maintain the files there :
1. Remove all files from STABLE commit then push.
2. Do the 'bug-fix' routine to update UNSTABLE. <-- here you will also remove the files from unstable.
3. Go to unstable and revert the commit where you deleted the files.
This way you keep them in Unstable, remove from stable and safely maintain the repositories going their separate ways.
ps: this is what I did here :-)
This reverts commit 4dbd5e476cbe441c2a9fa67e88c3b4dbf57b3b9e.
2011-07-05 13:32:21 -04:00
90f8de37d5
Merged bug fix from Stable into Unstable
2011-07-05 13:26:41 -04:00
cd53e5a131
Removing the ReduceReads files and package from the stable repo. It should only exist in private/unstable.
2011-07-05 13:22:55 -04:00
60b9aa7c59
Intemediate commit. Not working, but last changes are now logged before revisiting the DiffNode DiffElement DiffLeaf hierarchy
2011-07-05 09:10:34 -04:00
d787f43df7
Merged bug fix from Stable into Unstable
2011-07-05 01:04:28 -04:00
b38529309c
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-07-05 01:03:36 -04:00
e7e7cc390f
fixing a wrong refactor
2011-07-05 01:02:54 -04:00
8f5773fc5c
preparing the classes for future functionalities
2011-07-05 00:19:38 -04:00
3a8710b7de
Parsing and printing via simple oneLineString representations. X=Y, X=(A=B C=D), for example. Diff algorithm implementation, but no testing. DiffEngineUnitTest implemented, and testing framework nearly ready to actually evalute the correctness of the diff algorithm.
2011-07-04 23:43:49 -04:00
9124c84a7c
bug fixes
2011-07-04 21:10:44 -04:00
bb85f232b9
bug fixes
2011-07-04 21:04:49 -04:00
f26ffeaea0
bug fixes
2011-07-04 20:48:45 -04:00
04df153f47
bug fixes
2011-07-04 20:45:10 -04:00
7a04872a3f
bug fixes
2011-07-04 20:33:59 -04:00
08bc843d4c
SelectVariants can get a table to boost AF when choosing randomly
2011-07-04 20:23:22 -04:00
e634ef0599
Merge branch 'master' of ssh://delangel@nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-04 19:43:35 -04:00
527fbeaf3c
Extensive unit tests for DiffNodes, Diffelements, and DiffLeafs data structure. The lack of unity in these three data structures is a bit gross, to be honest, but it might may not be a significant factor when I reach implementing the generic diff functions. The problem is that ideally these would look like the scheme structures:
...
(A B (C D E))
which is a nested list containing A and B items and a sublist of C D E. Here there are only two classes: lists and everything else. Right now we have three. DiffNodes, which contain both atomic fields (A B) as well as the subnodes ((C D E)) here. These a specific class for DiffLeaf, which is really just a pair mapping name=value. And DiffElement contains a named item, since all objected in the hierarchy have a name. It's just doesn't feel right to me right now. Ultimately the problem is that you want the objects to be self-describing, so the DiffElement and DiffLeaf are a clean factoring the need for names in both the values and the nodes.
2011-07-04 19:34:15 -04:00
514b9c1751
UnifiedGenotyper already has @input/@output annotations
2011-07-04 19:23:05 -04:00
3206c581ce
Cleaning up the gatk jar argument, as queue now uses the queue's classpath.
2011-07-04 19:10:54 -04:00
980580287a
Fixing with the new variantcontext location
2011-07-04 19:06:06 -04:00
38740b0ff5
First working version of the DiffNode readers for VCF and BAM files. Unit tests confirm the readers are approximately working. Skeleton of a working DiffObjects walker that will be able to provide detailed information about how exactly two files of the same type differ, so long as the files are supported by the DiffNode structure.
2011-07-04 16:11:42 -04:00
983670e6ac
Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-03 15:57:34 -04:00
fac082de64
Report only highest AF and AC in multiallelic records in VariantsToTable or else R can't parse table
2011-07-03 14:32:12 -04:00
abe9480c6d
Merge branch 'master' of ssh://delangel@nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-02 21:19:15 -04:00
Guillermo del Angel
Mark DePristo
Eric Banks
Christopher Hartl
Khalid Shakir
Ryan Poplin
Mauricio Carneiro