03342c1fdd
Restructuring and interface change to ReadBackedPileup. We now lower support the Pileup interface, the BasicPileup static methods, and the ReadBackedPileup class. Now everything is a ReadBackedPileup and all methods to manipulate pileups are off of it. Also provides the recommended iterable() interface of pileup elements so you can use the syntax for (PileupElement p : pileup) and access directly from p.getBase() and p.getQual() and p.getSecondBase(). Only a few straggler walkers use the old style interface -- but those walkers will be retired soon. Documentation coming in the AM. Please everyone use the new syntax, it's safer, and will be more efficient as soon as the LocusIteratorByState directly emits the ReadBackedPileup for the Alignment context, as opposed to the current interface. In the process of the change over, discovered several bugs in the second-best base code due to things getting out of sync, but these changes were resolved manually. All other integrationtests passed without modification.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2154 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 03:51:41 +00:00
6fe1c337ff
Pileup cleanup; pooled caller v1
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2070 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-18 17:03:48 +00:00
21d1eba502
Cleaned division of responsibilities between arguments to map function. Reference has been changed
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from an array of bases to an object (ReferenceContext), and LocusContext has been renamed to reflect
the fact that it contains contextual information only about the alignments, not the locus in general.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1376 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-04 21:01:37 +00:00
761d70faa1
Better printing of multiple rods -- now produces a comma-separated set of values
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1289 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-21 21:58:27 +00:00
62807139fc
Cleanup pileup and depth of coverage in preparation for release. Add pileup, depth of coverage, and print reads to package for distribution.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1159 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-02 14:54:01 +00:00
fecba2cae5
Disabled option to show secondary quals as the definition has changed to conform to the spec and thus this printout is non-sensical.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@950 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 03:21:14 +00:00
13be846c2a
qualsAsInt argument for Pileup -- fixing stupid bug [again]
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@898 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 18:52:12 +00:00
97c8ff75dd
qualsAsInt argument for Pileup -- fixing stupid bug
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@897 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 18:51:17 +00:00
9de3e58aa8
qualsAsInt argument for Pileup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@896 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 18:37:39 +00:00
f2ea193149
For some reason the apostraphes in the comments were throwing annoying
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compile-time warnings: "unmappable character for encoding UTF8"
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@792 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 14:07:07 +00:00
65995887fc
Releasable version of the Pileup walker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@786 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 22:25:37 +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
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
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
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
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
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
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
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
4eac3193f7
Added RefMetaDataTracker system as a replacement for the List<RefenenceOrderedData> going into walkers. This system allows you to more easily get a tracker for processing using the lookup(name, default) system. See Pileup for an example.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@292 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-03 19:54:54 +00:00
385736469c
High performance pileup code and utilities
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@242 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-01 00:47:47 +00:00
d7c0bcc223
Reorganized GenomeLoc code to more clearly and better use the picard SequenceDictionary information.
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All GenomeLoc[] are not ArrayList<GenomeLoc> for clarity and consistency
Parsing now recursively merges contiguous elements chr1:1-10;chr1:11-20 => chr1:1-20
Added support for TraversingByLoci over all reference positions specified by the provided location array. System dynamically determines which traversal system to use.
Pileup now marks, very clearly, reference positions without covered reads.
Made changes around the codebase to deal with new GenomeLoc structure.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@218 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-28 20:37:27 +00:00
4a6be896b9
Provide out and err PrintStreams to the walkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@213 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-27 15:03:32 +00:00
3abaaa3cc3
Tried to add a poor man's version of seeing all reference sites in an interval, and failed. However, I did add the command line argument and a few pieces of useful code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@206 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-27 00:12:35 +00:00
5f9010116a
Collapse the walker hierarchy, in preparation for in-walker output streams less hokey walker args.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@201 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-26 16:22:35 +00:00
63cd1fe201
Push core / playground lower into the tree.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@160 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-23 23:19:54 +00:00
depristo
hanna
kiran
ebanks