f1de3d6366
Minor tweaks to how probs are supplied.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@676 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 19:47:41 +00:00
095dacd154
Experimental refactoring.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@675 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 19:46:50 +00:00
758f8aa89b
Experimental refactoring.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@674 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 19:46:34 +00:00
1518f8f9bf
Update training data creation in CovariateCounterWalker to output much smaller files by counting the number of occurences of each data point combination rather than outputting a line for each data point (i.e. each base). Also fixed bug in LogisticRecalibrationWalker where a null SAMHeader was being pulled from a function that is now marked deprecated.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@673 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 19:23:14 +00:00
4c12df372c
Dumb, dumb bug.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@672 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 19:21:33 +00:00
6e69193e3c
Deprecated calls to getSamReader on both the GenomeAnalysisEngine and the TraversalEngine. This call fails in the new style traversals, but it won't disapear until the cut-over to the new traversals is complete.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@671 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 18:52:42 +00:00
630066cc0a
1. Merge LocusWindows whose reads overlap.
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2. Fix bug (we weren't clearing the "to emit" list)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@670 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 17:33:23 +00:00
9f942fdfa0
Added code to correct the violation of the parsing interface. Now the analysis type resides in the command line arg, but is stored into the argument collection before it's passed to the genomeAnalysisEngine.
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Also fixed a bug where we'd exception-out if we didn't provide a interval region.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@669 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 15:33:55 +00:00
c4d89997ca
put in a dummy sample_name so it'll compile
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@668 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 15:12:42 +00:00
c8d7223789
do pooled calling properly for 1kg
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@667 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 15:12:13 +00:00
313a6d0fb5
lots of changes to facilitate calling indels and 1kG
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@666 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 15:11:42 +00:00
add7b6cf65
add sample_name to constructor, misc bug fixes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@665 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 15:10:17 +00:00
0267ccae7f
add code for computing indel genotype likelihoods
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make reference lods negative
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@664 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 15:09:29 +00:00
11723fbcc2
added method indelPileup. Generates a pileup of indel alleles given reads and ofsets (as from a locus walker).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@663 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 15:08:24 +00:00
ee9077fc69
LocusIterator iterated through LocusContexts, which was fine until now when we need something
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that iterates through loci (GenomeLocs). Rename LocusIterator to LocusContextIterator.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@662 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 13:54:57 +00:00
608948210c
Check for a reference before extraction.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@661 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 13:29:44 +00:00
32696b13f5
Fixed method override issue with old-style traversals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@660 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 01:22:18 +00:00
862b8a6787
intervals_file + genome_loc => intervals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@659 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 01:04:18 +00:00
0bca588629
Botched some boolean logic.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@658 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 22:53:52 +00:00
23e9e29964
Changed reads traversals from providing a LocusContext from which the reference sequence
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could be extracted to a char[] containing the reference bases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@657 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 22:45:11 +00:00
052819bed5
Switched dependencies of GenomeAnalysisTK to depend on GenomeAnalysisEngine.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@656 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 22:33:00 +00:00
ff1b92acc4
Switch over to the GenomeAnalysisEngine/CommandLineGATK system from the GenomeAnalysisTK code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@655 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 22:05:58 +00:00
009e71fcd9
We need to sort cleaned reads ourselves (instead of letting SAMFileWriter
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do it) because the SAM headers are often screwed up and claim to be
"unsorted". While here, I broke off the module from the SortSamIterator
in case someone else wants to use it.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@654 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 15:43:42 +00:00
c735e1f627
small javadoc cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@653 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 03:44:21 +00:00
e8b8ab5985
Added code to extend Matt's getReferenceBases out to the read walkers, so they can see the corresponding reference for each read.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@652 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 03:42:38 +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
898f65547e
Added code to split GenomeAnalysisTK.java into an object concerned with loading command line args, and one that runs the engines. This will allow us to run the GATK from other tools (like Matlab). Also some cleanup to seperate out the legacy traversals and the new style traversals. This is not live yet, and any modifications you need should be made to GenomeAnalysisTK.java for now.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@650 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 02:07:20 +00:00
8d43ec3d7e
a fix for a situation where a chromosome on the reference file contains no reads, and doesn't align to the bam file. This came up using reference 18, which has chomosomes like chr1_random that aren't in all BAM files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@649 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 01:39:25 +00:00
ee02b61068
added support for the argument collections code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@648 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-09 07:07:33 +00:00
742840017b
added the argument collection annotation for situations where fields in a command line args have embedded fields that should be checked for command line args
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@647 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-09 06:59:17 +00:00
55c1b688bd
Fix mediocre javadoc.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@646 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 22:31:16 +00:00
522f8b58be
Added second method for getting large sequences of the reference for use in reads traversals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@645 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 22:18:04 +00:00
517f27f331
Added sharding strat. code that picks the right kind of shard, based on the traversal engine
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@644 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 21:55:10 +00:00
6e394490cb
Cleanup in preparation for ByLoci traversal. Also did some work minimizing unit tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@643 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 21:27:54 +00:00
ee777c89de
Change the default mechanism for adding ROD bindings to the new system. TODO: create a new object type for these triplets.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@642 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 18:43:00 +00:00
3aabc144c6
Added functionality to allow for a contract between LocusWindowTraversalEngine and LocusWindowWalker which allows the Walker to act upon reads outside of the provided intervals.
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(Really, all we want to do is spit out all reads, but this allows the Walker to do other things with the reads if it wants)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@641 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 17:28:16 +00:00
de1c282e62
Reference-ordered data relies on bugs in the old command-line argument system to work. Update the ROD system to from -B track1 type1 file1 track2 type2 file2 to -B track1,type1,file1 -B track2,type2,file2.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@640 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 15:28:19 +00:00
483a58627b
More cleanup -- pushing shared functions down into the traversal engine.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@639 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 14:12:45 +00:00
7a9cfe1f75
Push reduceInit down a level so that the walker can call into it without weird casts.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@638 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 13:46:28 +00:00
a5154d99a3
Haven't heard any complaints, so I'm deleting the original implementation of TraverseByLociByReference. All TbyLbyR's will now go through the new sharding code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@637 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 13:37:00 +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
226edbdef6
Hypen-style xml output. Much sexier.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@635 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 01:04:40 +00:00
4c269b8496
Cleanup LinearMicroScheduler in preparation for TraverseByLoci inclusion.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@634 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 00:58:37 +00:00
21536df308
Change the sample XML marshalling code over to simple XML, and take out the castor lines in the ivy.xml
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@633 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 00:08:25 +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
a3d8febbf2
Error message cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@630 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 19:31:32 +00:00
c241d386a7
Beefed up command-line usage string.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@629 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 19:08:19 +00:00
5a6892900e
fixing oddities in duplicates
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@628 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:55:45 +00:00
4a26f35caa
new default syntax
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@627 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:16:53 +00:00
283a4d1b54
Fix some special-case cleaner issues.
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We now do the same as brute force in all examples to date.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@626 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:16:35 +00:00
93211c1cd8
template for windowmaker utility -- total non-functional
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@625 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:13:03 +00:00
2204be43eb
System for traversing duplicate reads, along with a walker to compute quality scores among duplicates and a smarter method to combine quality scores across duplicates -- v1
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@624 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:06:02 +00:00
71e8f47a6c
boundQual function for capping qual values
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@623 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:04:18 +00:00
e848f34896
countOccurances of char in string and max of a list of bytes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@622 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:03:49 +00:00
5a4bb76cc3
More capabilities for the pileup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@621 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:03:13 +00:00
89a26a7078
Utilities for handling duplicates
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@620 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:02:24 +00:00
4f85062004
Cleanup parsing method to make it less generic.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@619 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 16:21:17 +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
2f3ab53888
Oops. Arguments didn't load into applications with non-plugins (basically everything except the GATK).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@617 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 13:37:19 +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
752928df94
Switch to better mechanism for supplying a default.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@615 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 01:22:01 +00:00
dc944ec69b
First stage of ROD plumbing for MicroScheduler.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@614 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 23:26:21 +00:00
5136724884
Added code to the schedulers, one step closer to turning on the new reads traversals
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@613 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 22:36:25 +00:00
9c0b81e946
Default flags to 'not required'.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@612 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 22:09:49 +00:00
072808858e
added COUNT_CUTOFF arg: it is nor possible to tell the code to try to realign all read piles over trains of nearby indels with at least one indel observed in COUNT_CUTOFF or more different alignments (set the arg to 1 to realign around all indels); also, some diagnostic printouts added to the output (time spent on loading the reference, time spent on scrolling through the input bam file, counts of discarded reads)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@611 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 21:59:33 +00:00
1fe8155111
Some critical fixes for cases where argument values directly abut argument names
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and for arguments with missing short names.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@610 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 21:47:34 +00:00
0aba688e6f
Added a interface that all our SAMRecord iterators should try to code to. This is in the effort to keep our code generic
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@609 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 21:40:41 +00:00
62e7e46754
Miscellaneous cleanup. Better display of help output. Better exception subtyping. More thought-out access routines.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@608 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 21:16:01 +00:00
5be75e0ae6
First version of indel cleaner walker that works on intervals
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@607 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 20:20:48 +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
f5eae98af2
Fixed a bug where we could ask for a read when there were none in the pool (that's a bad thing).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@605 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 18:40:55 +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
98f4920739
Added BCEL and some basic instrumenation code to the test library.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@602 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 17:18:23 +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
4ac9e72739
Migrate default and GATK arguments over to new attribute system in preparation for conversion.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@600 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 23:57:48 +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
70afda12c4
Cut the test time down
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@596 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 22:05:51 +00:00
f5880109a7
Added TraverseReads test, some bug fixes discovered in the traversal test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@594 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 20:36:00 +00:00
daa2163ee8
Made the MergingSamIterator2 peekable. This iterator is being a ducktaped together swiss army knife, the iterators could use a redo soon.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@593 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 19:15:07 +00:00
09b0b6b57d
Fixes to try and speed up unmapped read traversals. Still not nearly as fast as they should be, but the next step would be to modify samtools code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@592 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 18:17:07 +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
8925df2e1e
More information from the duplicate combiner quality metrics
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@590 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-04 21:51:01 +00:00
2b6466ea00
coverage calculator based on Gabor's Pilot 3 Coverage Metrics
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@589 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-04 14:18:16 +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
6e38966349
Rename some key classes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@587 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 22:01:04 +00:00
5bdf653919
Cleanup: prepare for better output handling.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@586 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 21:40:46 +00:00
fd496159a8
Added convenience functions for RefHanger
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@585 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 21:14:40 +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
9f5f6f9bc7
N-way parallelism. Works for small test cases. Untested for large test cases.
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-Needs more comprehensive unit testing.
-Needs some basic refactoring.
-Needs rethink of interface boundaries.
-Needs to play more nicely in the /tmp sandbox.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@583 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 19:34:09 +00:00
df88c4d6b0
Added some code to determine the on-genotype and off-genotype secondary base distributions (which, at the moment, is commented out).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@582 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 06:48:19 +00:00
e7534b292f
Optionally applies secondary base distribution priors to normal single-sample genotyper posteriors.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@581 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 06:36:32 +00:00
58c80d8d87
For on and off-genotype primary bases, optionally compute the concordance of the secondary bases to their expected distributions. Each genotype has slightly different profiles.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@580 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 06:33:48 +00:00
16467ae7cf
A better (less overflow-y) implementation of multinomialProbability().
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@579 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 06:28:16 +00:00
4f818f5c1c
Choose a random base to stick in the pileup if the 2nd-best base matches the best base.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@578 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 06:27:37 +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
84dae06d5a
Initial version of ByDuplicates traversal, as well as a duplicate quality score estimator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@576 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 22:16:21 +00:00
ff420f5f6f
Enabled iterator() function
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@575 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 22:15:14 +00:00
12d6edfe7c
Only prints about first contig info setting
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@574 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 22:14:26 +00:00
1cc5e74435
More ways to access quality utils
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@573 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 22:12:07 +00:00
63403d32cd
Changes to the interface to the simple data source rippled out to a bunch of files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@572 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 20:35:56 +00:00
19e4e97f21
Add tag to ignore node class.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@571 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 20:27:34 +00:00
7f173af2ea
Encapsulate output tracking a bit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@570 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 15:12:13 +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
b630f2f2f1
More tables output by CovariateCounterWalker AND made CovariateCounterWalker and LogisticRecalibration aware of positive and negative strandedness of data which changes the regression output significantly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@568 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 01:22:50 +00:00
f7a877bfeb
Changed Sting exception from a base exception to a runtime exception. This makes it so you can throw it without the consumer having to check it, and hopefully people will be more inclined to use it.
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Please use this instead of throwing a plain runtime exception.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@567 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-29 22:09:41 +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
95d10ba314
Sketch of hierarchical reduce process, with unit tests for some core classes. Requires breakout of inner classes, testing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@565 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-29 20:26:16 +00:00
0a707a887b
Added ability to evaluate best + random base.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@564 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-29 20:05:36 +00:00
334f158e5a
added parameters for mapping quality and duplicate filters
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@563 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-29 18:05:34 +00:00
7de5da7065
Start getting the cleaner working in Walker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@561 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-29 14:59:53 +00:00
4c5f640eb7
Tweak the arguments passed to the command-line arguments parser so that it fails less often for invalid arguments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@560 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-29 14:36:27 +00:00
f557da0a78
Calculate interval-based statistics for Hybrid Selection
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@558 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-29 04:01:24 +00:00
6ecc43f385
Provide a default logger, some config settings, and some doc updates.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@557 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-29 02:06:05 +00:00
b836761104
removed the test cases from the bottom of this file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@556 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-28 21:50:22 +00:00
6b02248298
moved the test cases out of the GenomeAnalysisTK code and into a JUnit test case
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@555 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-28 21:49:17 +00:00
d4de68e260
added changes for the readsTraversal to accomidate design changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@553 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-28 19:49:58 +00:00
b6874f30cb
Added changes to bounded read iterator, it now explicitly takes a MSRI2 instead of the interfaces ClosableIterator<SAMRecord>. It would be good to fix this in the future with an interface that lets you get the (possibly merged) header.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@552 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-28 17:57:54 +00:00
395aaf48b0
Added the new by reads traversal, still needs to be sewn into the micromanager code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@551 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-28 17:55:08 +00:00
58b2578c44
Several changes to CovariateCounter walker to print more tables (called vs. observed Q scores), bug fixes to LogisticRecalibrationWalker and LogisticRegressor, and print string functionality added to Pair.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@550 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-28 00:37:48 +00:00
a0a581171b
print out the last interval
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@549 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-27 20:43:06 +00:00
a343f3eab7
Fixed bug where we weren't setting the reads group correctly. Also added code to set the printMetrics field of the singleSampleGenotyper from the Pool caller, it was null excepting out for me without that set.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@548 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-27 15:17:20 +00:00
1daf8e0987
A utility to compare the results of the SingleSampleGenotyper in 1-base and 4-base mode.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@547 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-27 15:10:08 +00:00
444bc18183
Removed binomialProb() method. Set better values for qHom, qHet, and qHomNonRef and allowed those to be set from the command-line.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@546 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-27 15:09:02 +00:00
b9c9dbb1d7
Added multinomialProbability method.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@545 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-27 15:03:50 +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
9a8902571c
Placeholder for parallel MicroManager.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@542 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-26 23:08:12 +00:00
1daa011387
Interval-based traversals were bleeding file handles. Fixed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@541 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-26 18:35:54 +00:00
1e2e78265d
Inadvertently removed interval file support in new TbLbR. Fixed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@540 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-26 18:15:42 +00:00
c9e9731495
More cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@539 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-26 17:46:52 +00:00
4036f24909
Documentation and cleanup work in preparation for parallelism.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@538 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-26 17:42:00 +00:00
0c76a70313
Renamed traversal by "interval" to "locusWindow"
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@537 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-26 02:26:08 +00:00
9a299c11d3
Oops, typo and build problems. FYI, fixing typos is better than packing...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@536 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-25 01:37:17 +00:00
ce470702fc
consistency with java naming conventions
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@535 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 21:44:48 +00:00
bfce0c93ab
removing bad file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@534 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 21:40:04 +00:00
05c6679321
Enabled ReduceByInterval
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@533 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 21:39:44 +00:00
ee2f022c71
Make new TraverseByLociByReference the default.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@532 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 19:50:11 +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
40a2b3eeb3
Basic logistic regression support for calibrating qualities; mostly for Andrew to experiment with
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@529 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 19:09:50 +00:00
061f4328b1
Covariate counter now outputs files used by R to do logistic regression.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@527 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 17:11:57 +00:00
4e4fd33584
First draft of actual pooled EM caller.
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Produces sane looking output on region of 1kG pilot1:
CALL NA12813.SRP000031.2009_02.bam CC 0.609084 0.609084
CALL NA12003.SRP000031.2009_02.bam CC 2.114234 2.114234 CCCCC
CALL NA06994.SRP000031.2009_02.bam CC 0.910114 0.910114 C
CALL NA18940.SRP000031.2009_02.bam CT 2.589749 0.910114 T
CALL NA18555.SRP000031.2009_02.bam CC 0.609084 0.609084
Next up, eval vs. Baseline pilot1 calls and pilot3 deep-coverage truth.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@526 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 13:43:41 +00:00
dd408a2a9a
First draft of actual pooled EM caller.
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Produces sane looking output on region of 1kG pilot1:
CALL NA12813.SRP000031.2009_02.bam CC 0.609084 0.609084
CALL NA12003.SRP000031.2009_02.bam CC 2.114234 2.114234 CCCCC
CALL NA06994.SRP000031.2009_02.bam CC 0.910114 0.910114 C
CALL NA18940.SRP000031.2009_02.bam CT 2.589749 0.910114 T
CALL NA18555.SRP000031.2009_02.bam CC 0.609084 0.609084
Next up, eval vs. Baseline pilot1 calls and pilot3 deep-coverage truth.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@525 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 13:42:15 +00:00
13d4692d2e
1. Added a by-interval traversal.
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2. Added a shell for the indel cleaner walker (it's currently being used to test the interval traversal).
3. Fixed small bug in downsampling (make sure to downsample the offsets too)
4. GenomeAnalysisTK.execute => anyone object to my change to "instanceof" instead of trying to catch a ClassCastException (yuck)?
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@524 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 04:33:35 +00:00
1984bb2d13
Made num_loci_total public because I'm lazy. I'll change it back later.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@523 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 03:57:23 +00:00
7ce11e152b
Simplified. Added option to perform four-base retest of a putative variant.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@522 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 03:56:15 +00:00
135d3eabeb
Now only distributes 80% of the residual probability to the secondary base, 10% each to the other two bases. Nicer labelling for stringified probability distribution output.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@521 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 03:34:43 +00:00
3cda85f2e3
New implementation of binomial probability that accurately computes values down to around 1e-237.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@520 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 03:32:04 +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
bd4cacb832
Added code to make a read group and sample name for BAM files that don't annotate them on reads. The defaults for both are now the filename, but this may be shortened in the future.
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The sample name for a read can be retrieved with the command:
read.getAttribute(SAMTag.RG.toString());
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@518 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 00:31:00 +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
635bfd8604
Added a little bit of hack to get the header back to the walker by initialization time, which was before sharding in the last version.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@516 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 21:07:11 +00:00
0208d201c7
Forgot this in the last commit...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@515 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 20:47:22 +00:00
3dc2afd7ab
Added the ability to get a merged header in a LociByReference traversal
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@514 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 20:34:52 +00:00
282f1d88b8
Make the operation 'read from the iterator and place on the queue' atomic with respect to hasNext(), next().
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@513 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 20:16:26 +00:00
998763950c
Oops, contig index is a zero not one based value
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@512 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 19:08:16 +00:00
8c13940c5a
A lot of changes to support by-read sharding and some from debugging of the by loci traversals
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@511 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 19:03:14 +00:00
32715a6c47
First check-in of walker that produces tables showing covariation of read cycle, and dinucleotide with quality score in a format usable for R analysis and for doing logistic regression.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@510 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 18:58:25 +00:00
0720d248ce
Adding the test case for by reads sharding of BAM data sources
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@509 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 18:01:22 +00:00
cae54ec52d
Walker for creating intervals to be used in the indel cleaner
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@508 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 17:58:19 +00:00
96db1477d4
I meant for default lod threshold to be 5.0, not 0.0.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@507 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 17:46:08 +00:00
ca66cccd2f
Privatized constructor to prevent instantiation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@506 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 17:45:39 +00:00
77e1e9e2f1
Added a static class to house useful math methods. All this has at the moment are methods for comparing doubles and floats, but I suggest that the bulk of our little math methods should be added here to avoid filling up Utils.java with so much random stuff.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@505 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 17:45:19 +00:00
3d7575bbb8
Oops...omitted walker.initialize().
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@504 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 17:35:28 +00:00
11e85f1969
Four-base mode now estimates the genotype using the one-base method and retests the site if the one-base method suggests the site is a het.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@503 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 17:23:24 +00:00
bd719f9c06
When checking that values are not infinite, also prints out the position so that I know which site was giving the error and I can just go there and debug it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@502 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 17:21:58 +00:00
efba30f1a1
Added a constructor in which the lod threshold can be set.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@501 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 17:20:48 +00:00
8c1905c7d9
Simple walker to print all of the sample names present in a merged bam file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@500 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 12:26:56 +00:00
a3a1c9dae8
Suppressed emission of duplicate paths through a four-base pileup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@498 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 21:08:45 +00:00
6cef8bd76c
added k-best quality path enumeration.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@497 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 20:26:51 +00:00
d99d67d51c
Refactored to clean it up a bit
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@495 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 19:18:46 +00:00
1bf4d040d8
Increase default shard size from 5 to 100000.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@494 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 18:29:44 +00:00
3af66a462e
Make PrintLocusContextWalker less verbose.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@493 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 18:28:02 +00:00
ffcd672c1c
Intermediate commit while working on getting four-base probs to work in the single sample genotyper. Has infrastructure for the new combinatorial approach and just choosing the best base more intelligently given a probability distribution over bases and the reference base.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@492 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 18:06:50 +00:00
4cafb95be8
TraverseByLoci / TraverseByLociByReference suffered from the same sam-triggered off-by-one (?) bug as TraverseByReference; it was just less obvious here because these versions don't shard.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@491 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 15:48:20 +00:00
cb2f621d01
reverting accidental commit of change to shard size
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@490 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 00:33:28 +00:00
b820130dce
* added ability to load multiple BAM files from command line
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@489 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 00:28:08 +00:00
5b8502745a
Added an epsilon (1e-4) to the tertiary and quaternary base hypotheses.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@488 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 00:01:37 +00:00
2ac240d78b
Removed an extraneous print statement.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@487 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 23:36:36 +00:00
0149c887ff
Fixed a bug wherein the residual probability was not being distributed properly when a file had secondary probs and the best and next-best base agreed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@486 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 23:36:09 +00:00
5abfc7d079
Added an argument ('extended' or 'ext') that outputs the four-base probs in a long format.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@485 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 22:27:26 +00:00
dac76f041b
Added some methods to retreive the probability distributions of individual bases.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@484 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 22:26:25 +00:00
5b2a7c9c23
Added some methods to complement a single simple base ([AaCcGgTt]) and reverse-complement a byte-array of bases.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@483 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 22:25:33 +00:00
521e202a10
updated interface
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@482 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 21:07:20 +00:00
55ca272919
reimplemented; now implements Genotype interface instead of AllelicVariant
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@481 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 21:06:42 +00:00
5f37ba8f26
now can be asked to log at INFO level all concordant or discordant sites, or both
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@480 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 21:03:44 +00:00
1f84b9647d
auxiliary data structure for mendelian concordance reporting; it's nice to have the latest version checked in in order for the code to compile...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@479 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 21:02:40 +00:00
ece3e9969e
one trivial walker to filter reads; bam in -> filter -> bam out
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@478 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 20:39:29 +00:00
61e855200d
latest version...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@477 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 20:38:37 +00:00
64b2fd866f
* extracted core quality-score based genotype likelihood code
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* precompute expensive operations (log/pow) based on Picard experience
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@476 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 18:58:43 +00:00
11c520b283
completed my old draft of the old school single sample genotype walker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@475 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 05:38:04 +00:00
b8233d92c8
Simple IO walker to test / crush file systems and evalute I/O performance in general
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@474 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-20 14:07:14 +00:00
bf76eab955
whoops; fix a comment line.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@473 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-19 17:54:54 +00:00
bcba1ff424
Fix a minor rounding bug and putz around with fractional counts in the pooled caller.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@472 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-19 17:52:24 +00:00
af6788fa3d
Misc:
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1. Added logGamma function to utils
2. Required asserts to be enabled in the allele caller (run with java -ea)
3. put checks and asserts of NaN and Infinity in AlleleFrequencyEstimate
4. Added option FRACTIONAL_COUNTS to the pooled caller (not working right yet)
AlleleFrequencyWalker:
5. Made FORCE_1BASE_PROBS not static in AlleleFrequencyWalker (an argument should never be static! Jeez.)
6. changed quality_precision to be 1e-4 (Q40)
7. don't adjust by quality_precision unless the qual is actually zero.
8. added more asserts for NaN and Infinity
9. put in a correction for zero probs in P_D_q
10. changed pG to be hardy-weinberg in the presence of an allele frequency prior (duh)
11. rewrote binomialProb() to not overflow on deep coverage
12. rewrote nchoosek() to behave right on deep coverage
13. put in some binomailProb() tests in the main() routine (they come out right when compared with R)
Hunt for loci where 4bp should change things:
14. added FindNonrandomSecondBestBasePiles walker.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@471 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-19 15:35:07 +00:00
eafb4633ba
Temporary workaround for samtools index bug: there seems to be an off-by-one error. Will file bug report.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@470 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 23:14:41 +00:00
758db73b98
Fixed SLOWNESS issue.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@469 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 20:10:34 +00:00
2a937fa8d3
set SAM file header's sorting order to unsorted, hopefully it will help to speed things up
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@468 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 19:32:24 +00:00
03ec3452f2
a first, simplest version of a walker that filters out reads based on user-specified criteria and writes remaining reads into a new bam file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@467 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 18:51:39 +00:00
f2f9fa3ed4
doc added
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@464 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 16:43:25 +00:00
d639ec3776
Remove some copied code to make sure the traversal engine stays in sync with the locus context provider.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@463 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 16:41:56 +00:00
df5aae5ed4
got read of a couple of warnings and added percentage(x,base) methods
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@462 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 15:15:21 +00:00
50ae1763f7
Support for -continue_after_errors flag in the validating pileup walker in case you want to see errors as they arise, rather than aborting greedily
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@461 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 03:13:11 +00:00
ee5ab9536f
trivial checking / flagging issues to enable testing of merging iterator performance
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@460 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 03:11:59 +00:00
dbf2344cef
Fixes for including duplicate reads in the locus traversal; now checks that the ref arg is provided when needed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@459 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 01:27:36 +00:00
01be8f09e3
Exception cleanup. All our non-runtime exceptions should extend from StingException, StingException needs to be lower in the tree to build.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@457 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 22:17:25 +00:00
e5c80e59dc
fixed the case when you're not seeking, it didn't initalize
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@456 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 22:16:03 +00:00
f47f640df6
Better debugging output and testing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@455 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 21:54:56 +00:00
165e504d1c
Turn on new TraverseLociByReference is now only dependent on the -et flag. REGION_STR does not matter.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@454 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 19:45:47 +00:00
12e1f192c4
Fixed a bug in this code where it would eat reads that didn't start at the beginning of the provided interval. This should fix / help fix Kristian problem
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@453 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 18:42:00 +00:00
835f1067d8
added isHom() and isHet() queries to the Genotype interface (with the obvious meaning)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@452 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 18:41:39 +00:00
55537c0d1e
chnage class name, now it compiles...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@451 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 16:51:00 +00:00
4f9bc7206f
some cleanup, also ensuring that all reads get written into output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@450 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 16:49:25 +00:00
e8a6cdb386
renamed standalone main
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@449 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 15:56:46 +00:00
832afd3d60
renamed standalone main
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@448 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 15:56:27 +00:00
85308f4ddc
resurrected indel tool's standalone main
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@447 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 15:55:52 +00:00
6f56938d42
* added a bit more debugging output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@446 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 15:20:26 +00:00
d35a542bb9
* fixed bug where the merged header was not being set on the read (although the read group was)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@445 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 12:53:07 +00:00
240eb18564
fix a few related issues when not all the reads were written into the output files. now cleaned output still contains all reads either with modified alignments or untouched
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@444 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 03:56:47 +00:00
0d324354ae
separate interface for genotypes as opposed to (population) allelic variants
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@443 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 03:55:16 +00:00
7e05b43f40
* added some error checking for read groups
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@442 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 03:22:49 +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
7261787b71
Fixed potential bug with next() operation returning empty contexts when a read contains a large deletion. We can now use the look ahead safely...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@438 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 21:38:28 +00:00
e70aecf518
bug fix, but important
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@437 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 21:07:20 +00:00
76d833e39b
Meaningful assert messages
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@435 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 19:12:28 +00:00
67ea66c866
Bug fix
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@434 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 19:12:18 +00:00
1edfe48194
Better debugging output with .debug
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@433 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 19:09:18 +00:00
9cc808104e
Fixed subtle bug in permitting EXPAND_WINDOW to be > 1. We now use the right window size so we avoid including empty hangers. There's still a rare bug to sort out, which occurs in the case where a read with an indel can generate empty hangers.
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Also cleaned up the debugging output.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@432 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 19:08:26 +00:00
180ff13290
Added a bunch of changes to support the new MicroManager code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@431 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 18:29:38 +00:00
339261c4a9
Load the dictionary and sanity check it against the index.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@430 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 18:04:13 +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
3fda8613c3
* minor formatting changes
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* support for "extended" output
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@428 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 15:11:05 +00:00
12407b5b1a
Deleted the old file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@427 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 13:55:01 +00:00
6db9127f90
Added changes to shattering, refactored SAMBAM into SAM
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@426 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 13:52:56 +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
7949e377e4
Intermediate commit. Refactored some simple base manipulation stuff into BaseUtils.java. Generalized some likelihood computation logic to make future possible EM-ing easier.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@424 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 04:18:07 +00:00
d0b8d311e6
Can now optionally print the read and the alignment region of the reference.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@423 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 04:10:30 +00:00
d4aaa1bef4
* fixed (with Matt's help) the argument parsing
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* outputting UCSC wiggle format
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@422 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 02:17:39 +00:00
24722a442e
Slight code cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@421 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 22:21:36 +00:00
e6fb122d7d
Added some fixes and new iterator tests
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--This lin e, and those below, will be ignored--
A gatk/iterators
AM gatk/iterators/BoundedReadIteratorTest.java
M gatk/dataSources/simpleDataSources/SAMBAMDataSourceTest.java
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@420 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 22:19:36 +00:00
13b0995d54
Adding an iterator that bounds the number of reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@419 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 22:18:31 +00:00
72a3d84ed2
General purpose pileup code -- you can use these features to obtain detailed pileup data from reads and offsets. Useful for all pileup based walkers. Expanded support for rodSAMPileup to enable the new ValidatingPileupWalker, which takes a samtools pileup output and checks that GATK gives identical output as samtools on a per base and per qual pileup. It's going to be a very useful validation tool.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@418 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 22:13:10 +00:00
baae98c6d5
and don't allocate new 200M string every time please, just pass byte array!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@417 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 21:55:33 +00:00
9d56355abe
bug fixed when reference name was passed as a string instead of actual reference bases
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@416 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 21:46:27 +00:00
222c4e5865
Commented out some debugging lines
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@415 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 20:15:41 +00:00
49d76014d1
Commented out a debugging line
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@414 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 20:15:11 +00:00
b39e584787
Primary or secondary bases that got a quality score of literally zero led to unfortunate infinities. Added an epsilon (1e-5) to every prob.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@413 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 20:04:49 +00:00
d28e9f9b98
search over q's for finding argmax[q] p(D|q)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@412 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 19:15:45 +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
647827b18c
Transitioned indel code to use GATK and Walkers
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@410 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 19:14:15 +00:00
b363eedd2c
Deal with screwy reads by changing logic to determine whether we are
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past the last interval
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@409 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 19:13:16 +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
88ebf1a05b
Fied some documentation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@406 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 17:41:38 +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
704f1bd634
It helps if I check the new base class in with my changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@404 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 17:18:16 +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
961dbbd4ef
Now output bases and qhat and qstar into the GFF.
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Quals coming soon (four-base)
QHAT : Most likely alt allele freq (unconstrained by number of chromosomes).
QSTAR : Most likely alt allele freq (constrained by number of chromosomes).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@402 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 15:23:00 +00:00
dafdff1974
All bases are now indexed as A:0, C:1, G:2, T:3.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@401 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 14:49:43 +00:00
40ea22eb17
Added some methods to return the cross-talk partner base of a given base or base index.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@400 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 14:49:12 +00:00
eb4b4a053b
A bunch of updates to the SAM/BAM data source, along with test cases for the merging of multiple files (it works!).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@399 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 14:19:20 +00:00
30121534ed
Outputs the secondary bases and quals (if available) in verbose mode. Prefixed with the tag 'SQ='.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@398 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 13:58:28 +00:00
998fad76c6
Some utility methods for creating pileups of secondary bases and secondary quals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@397 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 13:57:54 +00:00
8b2c2e677b
Uses the cleaner new GenomeLoc(read) syntax
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@396 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 00:55:43 +00:00
1cee7948ab
Added lots of assertions to check for problems.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@395 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 00:55:19 +00:00
794360c410
Added verbose option to show mapping qualities and base qualities as ints!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@394 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 00:54:48 +00:00
cc75e8f712
Uses the cleaner new GenomeLoc(read) syntax
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@393 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 00:53:58 +00:00
11377ef390
Added lots of assertions to check for problems. The current GenomeLoc needs to be cleaned up and refactored but at least it runs. We need unit tests ASAP
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@392 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 00:53:08 +00:00
bb666ce392
Added mappingQualPileup function for use in the verbose mode of Pileup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@391 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 00:51:26 +00:00
bc43c0eefc
there are really cases when we can not merge until we get just two pilesant now we do not crash in those cases but print a warning and just show the resulting n piles even when n>2
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@390 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 00:45:47 +00:00
8e6093d5a5
remove mom/dad/kid cmd line arguments that were needed for mendelian walker; now we can use generic track binding!!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@389 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 00:45:34 +00:00
f838a5e511
Changed some double comparisons of the form a == b to abs(a - b) <= precision. Now we shouldn't be passing or failing some if conditions due to floating-point precision.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@388 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 20:05:46 +00:00
887adcfc7f
Some minor fixes to the last check-in
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@387 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 18:24:51 +00:00
f2d0d73309
removed old shard strategy code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@386 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 18:13:45 +00:00
dd604799dc
Added some new code for shard support over reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@385 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 18:11:43 +00:00
d44c30154a
added MAX_READ_LENGTH - now we can ignore long reads (454?); a bad idea in general, but the performance hit is to hard to take, at least for preliminary testing runs...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@384 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 16:53:12 +00:00
e91a429c58
A class to print out as much context about the given locus site as is possible. Useful for testing traversal engines -- run old and new code across a given region and diff the output to make sure they have the same context.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@383 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 15:29:55 +00:00
6652f13a17
more verbose gff output!
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EVEN MORE verbosity to come!
Tremble in anticipation.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@382 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 15:21:23 +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
6e180ed44e
Unified caller is go.
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AlleleFrequencyWalker and related classes work equally well for 2 or 200 chromosomes.
Single Sample Calling:
Allele Frequency Metrics (LOD >= 5)
-------------------------------------------------
Total loci : 171575
Total called with confidence : 168615 (98.27%)
Number of variants : 111 (0.07%) (1/1519)
Fraction of variant sites in dbSNP : 87.39%
-------------------------------------------------
Hapmap metrics are coming up all zero. Will fix.
Pooled Calling:
AAF r-squared after EM is 0.99.
AAF r-squared after EM for alleles < 20% (in pools of ~100-200 chromosomes) is 0.95 (0.75 before EM)
Still not using fractional genotype counts in EM. That should improve r-squared for low frequency alleles.
Chores still outstanding:
- make a real pooled caller walker (as opposed to my experiment framework).
- add fractional genotype counts to EM cycle.
- add pool metrics to the metrics class? *shrug* we don't really have truth outside of a contrived experiment...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@380 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 12:29:51 +00:00
f39092526d
Added function RandomSubset
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@379 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 12:14:53 +00:00
b4136b6d6e
a few tweaks to make it more robust: ignore reads with cigars containing anything but I,D,M; don't set up contig ordering manually, rely upon reference sequence and its dictionary; don't die if a record does not have NM tag, but faal back to direct counting instead; now requires reference as a cmdline arg
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@378 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 04:49:19 +00:00
756e6c61d8
Strictness args are presented as lowercase in the help, but only accepted if uppercase. Changed help to list the valid arguments in uppercase.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@376 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 00:50:19 +00:00
c51f51f255
Make sure we always write at least 1000 points per base in each cycle's scatterplot. Print the disagreement rate between Bustard and FourBaseRecaller.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@375 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 00:49:41 +00:00
1fb16d54e0
For SAM files that have no alignments and when no reference is specified, contigInfo.getSequence() is null, causing an error when getSequenceName() is called on the resulting null pointer. Check for null instead and return that instead of barfing here.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@374 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 00:48:21 +00:00
5e96ab6161
Helpful functions for converting a base (char) to a base index (A:0, C:1, G:2, T:3, alphabetical and consistent with Illumina conventions to minimize confusion.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@373 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 00:46:23 +00:00
35fc002d5d
Debugging information is now written in such a way to make it easier to import into R.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@372 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-12 19:45:33 +00:00
6ee4fe5a20
Fixed a Bustard/Firecrest file synchronization bug.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@371 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-12 19:44:07 +00:00
817278be46
If a SAMRecord is on the negative strand, reverse complement the SQ tag.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@370 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-12 19:42:24 +00:00
1d5a22cacf
Extracts a Fastq file and the SQ tags to a separate file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@369 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-12 19:41:44 +00:00
e410c005c0
A debugging tool to ensure the SQ tag in a four-prob SAM file matches the SAMRecord strand orientation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@368 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-12 19:40:42 +00:00
9c37400c4f
Added basic performance testing so I can make sure concurrent access doesn't slow down overall fasta access.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@367 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-12 18:05:56 +00:00
c7777d46d6
* re-enabled setting of sequence dictionary information on GenomeLoc
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@366 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-12 02:44:14 +00:00
ce72932a45
* refactored GenomeLoc to use contigIndex internally for performance and fixed several calling classes
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* added basic unit test for GenomeLoc
* fixed bug when parsing genome locations like chr1:5000 the start position was being left as maxint rather than being set to the same as the stop position.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@365 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-12 02:25:17 +00:00
49fd951d8c
Initial test suite for FastaSequenceFile2, so I can add parallelism support with abandon.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@364 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-11 21:10:42 +00:00
608a66e6ab
TbyLocibyRef previously didn't seem to support traversals with no interval specified. Put in a temporary fix until the threaded approach is in place.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@363 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-10 22:14:06 +00:00
c2669021b8
Cleanup, and support either by-interval traversals or full traversals in data source-backed code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@362 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-10 22:09:01 +00:00
2322bb7d86
Workaround: use a single ReferenceIterator for an entire micromanaged traversal. We'll have to
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do something about ReferenceIterator thread safety later.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@361 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-10 20:50:28 +00:00
95753e1b34
Should've been calling queryOverlapping in locus mode.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@360 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-10 20:22:04 +00:00
2b59110dca
CombineSamAndFourProbs is better.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@358 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-10 04:19:53 +00:00
56aa98ad30
Ignore null values.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@357 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-10 04:18:20 +00:00
2ef2c9e121
Fixed an issue wherein the SQ field was only being pulled from the first read of the pileup, no matter what. Fixed an issue wherein Andrew enumerates his bases as A:0, C:1, T:2, G:3, and Kiran's QualityUtils methods enumerate bases as A:0, C:1, G:2, T:3 (we should standardize this). Fixed an issue wherein the remaining probability was being divided by 3 rather than 2 when four-base probs are enabled.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@356 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-10 04:17:53 +00:00
17b3d5b554
New ROD accessing system, including a generalized interface for binding ROD on the command line that doesn't require you to chance GenomeAnalysisTK.java
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@355 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 22:04:59 +00:00
f5cc2d8b0b
Commented out import of IlluminaParser.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@354 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 21:30:29 +00:00
0d825ccfc1
Oops. Fixed duplicate reference to the reference.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@353 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 21:27:57 +00:00
9afa101465
Add interval support to the
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.__ __ __
_____| |__ _____ _/ |__/ |_ ___________
/ ___/ | \\__ \\ __\ __\/ __ \_ __ \
\___ \| Y \/ __ \| | | | \ ___/| | \/
/____ >___| (____ /__| |__| \___ >__|
\/ \/ \/ \/
classes!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@352 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 21:23:43 +00:00
c5220c0822
Four-base probs are now decoded with the relevant method in QualityUtils
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@351 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 20:52:17 +00:00
9bc763a835
A better (aka 'working') tool for combining four-base probs with an aligned sam file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@350 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 20:51:37 +00:00
b7a2e82b46
Can optionally process raw or corrected intensities.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@349 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 20:50:11 +00:00
6cdad10dd1
Make output type identical to the bustard parser so the values can be easily swapped for one another.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@348 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 20:49:34 +00:00
d0ce56e018
Remember to take the strand flag into account when calculating error rate per cycle as a surrogate for instrument performance.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@347 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 20:48:45 +00:00
8a1207e4db
Bringing up scaffolding for integration of locus traversals by reference with Aaron's data source code.
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Reverts to original TraverseByLociByReference behavior unless a special combination of command-line flags are used.
Lightly tested at best, and major flaws include:
- MicroManager is not doing MicroScheduling right now; it's driving the traversals.
- New database-ish data providers imply by their interface that they're stateless, but they're highly stateful.
- Using static objects to circumvent encapsulation.
- Code duplication is rampant.
- Plus more!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@346 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 20:28:17 +00:00
8e2f5471a1
Some cleanup to the data source, and another JUnit test case.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@344 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 14:58:05 +00:00
d56193b6df
Cleanup of a couple of output statements
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@343 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 14:09:07 +00:00
c556a97f17
Skeleton of Somatic Coverage tool
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@342 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 02:34:03 +00:00
12752cf893
Added a bunch of fixes: MSRI wasn't working, sharding had broken edge cases, and SAMBAM DS needed to close the file handles.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@341 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 00:20:15 +00:00
089bf30cf4
Send things to the out file via the logger.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@339 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 21:49:03 +00:00
6db9a00a0b
SAMFileWriter doesn't appear to flush the buffer when its destructor is called. You have to call the close() method. Also, choose a random base for Ns in the forward and reverse strands so that samtools doesn't pitch a fit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@338 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 21:48:24 +00:00
eb2f0ebd62
If the first base of a read is 'N', and the alignment cigar says every base matches, samtools calls shennanigans. Now I just output an A, but the real way to do this is to modify the cigar string accordingly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@337 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 19:58:18 +00:00
0e7d962eca
Oops. Slight twiddle of the math here so that I'm not asking if bestBase == nextBestBase.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@336 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 19:56:54 +00:00
d4ab95c098
Added a constructor, took out a copy constructor, and changed some SAMBAM code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@335 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 19:53:20 +00:00
0b81a76420
added support for Picard IntervalList files to --interval_file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@334 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 16:49:43 +00:00
295c269a64
Remove the main() I put in for debugging
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@333 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 16:43:44 +00:00
d517245beb
Fixes for shattering, added JUnit test case
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@332 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 16:37:34 +00:00
62ac7366ed
A quick hack to ensure that the sequence, qualities, and secondary qualities are in accordance with the strand flag.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@331 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 15:57:28 +00:00
25474ebe7e
Computes the read error rate for a bam file. Ignores reads with indels, treats low-quality and high-quality reference bases the same. Does not count ambiguous reference bases as mismatches. Optionally allows for best two bases in read to be used.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@330 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 15:56:10 +00:00
59b2e6a90f
Added some stuff for retreiving the base index and probability of a compressed base.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@329 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 15:52:58 +00:00
8d48bdc9ec
it walks... the version committed actually counts snps only
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@328 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 02:00:41 +00:00
62d75ced3c
nothing fancy, just a wrapper (aka struct) to pass around a bunch of counts
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@327 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 01:58:57 +00:00
453d13415d
count variant as biallelic if it's just a non-ref homogeneous site!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@326 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 01:57:27 +00:00
b49f713336
Enabled multiple argument for GATK driver; first step towards generalized -rods <name> <type> <file> argument structure
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@325 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 01:52:13 +00:00
1ade22121b
cruel hack: new toolkit-wide optional cmdline arguments added to allow for loading trio genotyping tracks; to be moved back to walker when walkers can register their data needs with the toolkit
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@324 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 22:33:26 +00:00
8ec427ab66
latest version... still under dev/testing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@323 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 22:31:06 +00:00
202c501939
Added a sample xml marshaller / unmarshaller.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@322 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 22:28:16 +00:00
00722e19bc
The system now requires a dictionary file for a fasta file, or it throws an error. You can't just operate without a sequence dictionary any longer. We will transition to a GenomeLoc system that assumes a dictionary is available.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@319 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 22:19:54 +00:00
9c4fc633aa
Make it symmetric: if there is no sequence dictionary, also send a message to the logger, just like we do when we find the dict
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@318 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 21:44:39 +00:00
b64e4d1a04
seekForwardOffset changed (improved?): first, compareContigs does *not*, in general, return -1,0 or 1 if no dictionary is available; second, be more flexible in trying to jump to the right contig (current implementation of FastaFile2 will still through an exception if there's no dictionary, but iterator itself behaves transparently)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@317 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 21:42:33 +00:00
2663ac3e4a
documentation fix
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@316 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 21:39:50 +00:00
8a357a88a2
right...exponential should be exponential, so I might want to increment the exponent
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@315 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 20:12:05 +00:00
6ce9e0f941
delete the old strategy
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@314 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 19:40:03 +00:00
08fddd43af
-Replaced adaptive and linear strategies with an adaptive linear strategy
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-Added the exponential growth strategy
-Added factory code that allows you to transitition between strategies, so if you want to move from linear to exp at a point, and then back when you've hit a runtime threshold, it will take care of it for you.
-Changed the code to return a Shard instead of a GenomeLoc
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@313 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 19:37:38 +00:00
6369d23b43
renamed; these files are more strategy than actual shards
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@312 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 16:50:56 +00:00
e95f427965
Added isReference() to AllelicVariant and updated rodDbSNP accordingly
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@311 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 14:49:20 +00:00
99579a1ef8
Math correction.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@310 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 02:18:13 +00:00
9be978e006
Intermediate commit (debugging info).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@309 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 01:20:15 +00:00
b42d8df646
the new shatter method, independent of the underlying data. The only thing needed to create a Shard is the reference seq, which may be a problem in reference less traversals, so the builder class is there so we can make different construction schemes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@308 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 00:32:57 +00:00
0baa8c0f76
We need a base exception so we can differentiate between exceptions we've generated and those external to our code. All our exceptions should extend this exception. I'll migrate the ones I can find later on.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@307 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 00:13:45 +00:00
150bca30aa
typO in the documentation...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@306 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-06 23:05:59 +00:00
4aa9c0d591
Matt make a good point that the Reference Iterator we were using wasn't bounded; The BoundedReferenceIterator takes a GenomeLoc to bound the iterations by
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@305 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-06 23:03:56 +00:00
kiran
andrewk
ebanks
aaron
jmaguire
hanna
depristo
asivache
kcibul