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.
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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.
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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
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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)
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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()
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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.
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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
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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
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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.
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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...
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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.
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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
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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
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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.
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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
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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).
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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.
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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.
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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.
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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.
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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...
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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
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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
ec0261275b
Lots of command line argument validation. Catches all common validation problems, including missing required arguments, invalid arguments, and several types of misplaced argument value errors.
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Still pending:
- Help system.
- Mutually exclusive arguments.
- Design includes too many classes per file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@597 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 22:08:00 +00:00
6550fe6f97
Another pass of command-line arguments. Revised parser supports all types
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of arguments that the existing parser supports, but does a poor job with
validation.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@591 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-04 22:41:23 +00:00
4f2ccda56a
Interface skeleton for a new command line argument parser. Nowhere near the point of being a drop-in replacement for apache cli yet.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@588 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-04 00:11:42 +00:00
7ed496b859
JUnit test for RefHanger
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@584 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 20:11:14 +00:00
9800d09608
A more thorough test for multinomialProbability.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@577 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 06:27:05 +00:00
3bf3c21ddd
Changed the assert code in the genome loc to throw exceptions, and deleted a function no one seems to be using.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@569 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 13:54:51 +00:00
ba9a0b5da8
Break out some of the weird inner classes out of the HierachicalMicroScheduler.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@566 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-29 21:07:07 +00:00
eeb0b78cce
Added another assert to testBinomialProbability() and added a test method for testMultinomialProbability().
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@544 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-27 14:59:11 +00:00
e50ae97fe1
Introduce new index-based fasta reader. Clean up MicroManager code, pushing necessary code back into TraversalEngine.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@531 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 19:40:21 +00:00
305584b69e
Test class for MathUtils with a test for binomialProbability().
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@519 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 03:31:02 +00:00
45d962e491
I understood the contig index incorrectly when I initially wrote this code. Fixed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@517 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 22:31:43 +00:00
56f6847456
Changed interface from contig,pos,length to more common contig,start,stop interface.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@441 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 00:04:41 +00:00
26e84d7fd6
Added index iteration for ReferenceSequenceFile interface compatibility.
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Added better error checking for querying past the end of a contig.
Lots more testing.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@429 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 17:17:11 +00:00
182626576f
Basic indexed fasta POC in place. Requires a more complete implementation of the ReferenceSequenceFile interface,
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and much more testing.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@425 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 13:46:56 +00:00
96248cdec4
Added some output to all the classes, including build in runtime analysis
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@411 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 19:14:53 +00:00
0629f79049
Moved fasta support files into their own package.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@408 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 18:13:23 +00:00
7a4a5a17c0
Made sequence index compatible with Aaron's junit changes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@407 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 17:53:20 +00:00
186c799ffc
Class to read an .fai file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@405 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 17:37:18 +00:00
4b3578e1de
Added the base test case, fixed the rest of the test cases to follow suit. Added more verbose output to ant for junit tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@403 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 17:11:38 +00:00
cf929a8275
Get rid of test case's dependence on transient methods.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@381 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 15:16:42 +00:00
hanna
aaron
kiran
depristo