8eeb87af2a
Tests for downsampling related utilities in ListUtils class that didn't get checked in earlier
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1352 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-31 00:09:35 +00:00
bca894ebce
Adding the intial changes for the new Genotyping interface. The bullet points are:
...
- SSG is much simpler now
- GeliText has been added as a GenotypeWriter
- AlleleFrequencyWalker will be deleted when I untangle the AlleleMetric's dependance on it
- GenotypeLikelihoods now implements GenotypeGenerator, but could still use cleanup
There is still a lot more work to do, but this is a good initial check-in.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1335 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-29 19:43:59 +00:00
b4adb5133a
GLF rod as a AllelicVariant object.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1282 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-21 00:55:52 +00:00
9ecb3e0015
adding GLFRods with tests and some other code changes
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1251 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-15 15:30:19 +00:00
36819ed908
Initial changes to the SSG to output GLF by default
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1231 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-14 08:46:04 +00:00
e4152af387
added a big speed-up for interval list input processing. With large interval sets this was taking way too long...
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1227 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-13 22:00:00 +00:00
b61f9af4d7
Cleaning up, preparing to incorporate a better fix for Eric's problems with validation stringency in BAM files opened directly from the walkers.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1222 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-13 01:42:13 +00:00
8ee5c7de8e
GLF reader and writer check in.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1202 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 23:06:37 +00:00
da4d26b1ea
Enum support for command-line argument system, and some cleanup for hacks to the CleanedReadInjector that were required because Enum support was missing.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1199 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 20:26:16 +00:00
433ad1f060
Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1196 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 18:49:08 +00:00
194b75613b
Fix compile problem with unit tests.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1187 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-07 20:29:31 +00:00
f6a273a537
other fixes for some broken unit tests
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1181 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-07 05:53:13 +00:00
d19366eaad
Cleanup emergency fixes for out-of-bounds issues in reference retrieval. Fix spelling mistakes.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1173 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-06 15:41:30 +00:00
d4d3af20f2
made a fake fasta generator, so we can now generate a complete bam / fasta combo of made up data.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1150 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 21:35:34 +00:00
f5cba5a6bb
Fixed genome loc to be immutable, the only way to now change it's values is through the GenomeLocParser.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1132 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 19:17:24 +00:00
d7d4298917
Some files to support generic genotype outputing
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1112 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-26 15:43:41 +00:00
5b1c23a7f2
changes to fix and test the interval based traversals
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1095 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 17:54:15 +00:00
bcb64d92e9
Aaron: 1, GenomeLoc: 0. I changed our GenomeLoc class, seperating the creation of a genome loc (with the reference setup) to a parser class. GenomeLoc now just represents the actual genomic postion. The constructors are now package-protected (to enforce using the parser), but we may want to expose some constructors in the future.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1069 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-22 14:39:41 +00:00
8ac40e8e2d
Updated version of the recalibration tool
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1060 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-19 17:45:47 +00:00
6ee64c7e43
added changes to support alec toUnmappedRead seek. Huge improvements (orders of magnitude) in unmapped read performance.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1021 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-16 22:15:56 +00:00
71e3825fa1
First pass of a walker for Eric that searches through an input BAM file for unclean reads, injecting the cleaned reads in their place and outputting the composite result.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@989 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 20:18:13 +00:00
195b4ea7b4
a rename for consistancy of Sam to SAM, creating a genotype utils dir, and moving the GLF code into it.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@984 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 17:46:06 +00:00
36c98b9d6c
added tools to test read based traversals using the artificial in-memory SAM file tools, and testing of the PrintReadsWalker
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@957 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 01:52:25 +00:00
eb962fe52a
adding an artificial sam file writer, used to unit test some of the walkers (mainly the PrintReadsWalker)
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@956 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 21:47:49 +00:00
af0b03a257
Added tests for mostFrequentBaseFraction() and reverseComplementString()
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@944 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 00:53:45 +00:00
109bef6c08
We're no longer in the read-dropping business.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@901 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 22:37:51 +00:00
82aa0533b8
added some more documentation to the GLF writer and it's supporting classes, and some other fixes
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@875 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 14:53:58 +00:00
e712d69382
GLF writing support
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@872 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-01 21:30:18 +00:00
b43deda6c9
iterative changes to GLF files; also a test of checking-in over sshfs.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@850 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-28 20:24:30 +00:00
5e8c08ee63
Update to latest version of picard. Change imports in all classes dependent on picard public from import edu.mit.broad.picard... to import net.sf.picard...
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@849 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-28 20:13:01 +00:00
d275c18e58
adding some objects we need for the GLF format.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@846 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 22:32:25 +00:00
d994544c47
Added back end code support for Sharding based on genomic location for reads. Changed the sharding
...
code to take GenomeLocSortedSet instead of a list<GenomeLoc>, and added a bunch of much simplier
and cleaner test cases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@816 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 20:57:46 +00:00
d056f9f3e8
Changed the name to reflect the sorted nature of the set, added some fixes
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@810 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 22:34:24 +00:00
831d430025
Added a collection for storing GenomeLocs, that also has functions for removing by genomic region (that may span multiple GenomeLoc's in the collection), and adding regions, which are then merged with any overlapping regions.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@809 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 21:52:40 +00:00
7a979859a9
Intermediate checking for evaluation -- now supports transition / transversion evaluation
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@793 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:05:06 +00:00
bdf772f017
Added test for determining the fraction of a sequence that's taken up by the most frequent base (quick-and-dirty homopolymer testing).
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@780 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 20:35:08 +00:00
324ef9cbd1
Test class for PathUtils.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@773 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 19:31:22 +00:00
7161b8f927
Disable support for short name values directly abutting their arguments.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@740 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 16:09:32 +00:00
d14cab0be7
Added IterableLocusContextQueue and test. Cleaned up tests, adding BaseTest where it didn't exist. Enhanced test runner to run only classes ending in ...Test.java, so that utility classes can sit alongside the tests but won't be run by JUnit.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@693 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-13 21:32:05 +00:00
4ce3feba4d
my move ended up being a copy, so this is to delete dupplicate files.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@651 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 02:10:26 +00:00
bae4256574
Started the process to make the GATK engine into a runnable object so we can call it from other processes. Step 1: make a configuration object that can serialize to and from an XML file. This way we can store the information everyone uses shell scripts for. Also we can now pull the list of params out of the GenomeAnalysisTK.java. More to come...
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@636 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 01:25:26 +00:00
7f8850a8a2
Argument validation.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@631 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 20:28:56 +00:00
d725c6cf1c
Added unit tests for parsing failures that I encountered during integration testing.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@618 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 14:01:54 +00:00
4177560543
Mutually exclusive options.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@616 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 13:27:48 +00:00
98716138e9
Cleanup: add support for non-public fields. Track matches as state of parsing engine as well as definitions.
...
Made fields of command-line argument system non-public by default.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@606 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 19:38:05 +00:00
ef211f96b1
Remove old Apache CLI-based arg system.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@604 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 18:37:51 +00:00
521aa40baa
Bring new command-line argument parsing system live.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@603 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 18:16:11 +00:00
bfd6dfe36c
Added real-world tests and tests for conditional validation.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@601 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 13:38:46 +00:00
2ee9374975
Check for proper error output in case of boolean args with parameter specified.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@599 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 23:08:48 +00:00
b0cdba8bb3
Acting on Kiran's suggestion to make the doc tag in the @Argument annotation required.x
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@598 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 22:43:40 +00:00
andrewk
aaron
hanna
depristo
kiran