862b8a6787
intervals_file + genome_loc => intervals.
...
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
23e9e29964
Changed reads traversals from providing a LocusContext from which the reference sequence
...
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.
...
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
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.
...
(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
7a9cfe1f75
Push reduceInit down a level so that the walker can call into it without weird casts.
...
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
7f8850a8a2
Argument validation.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@631 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 20:28:56 +00:00
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
...
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
752928df94
Switch to better mechanism for supplying a default.
...
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.
...
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
...
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.
...
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
9f5f6f9bc7
N-way parallelism. Works for small test cases. Untested for large test cases.
...
-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
84dae06d5a
Initial version of ByDuplicates traversal, as well as a duplicate quality score estimator
...
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
7f173af2ea
Encapsulate output tracking a bit.
...
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
6ecc43f385
Provide a default logger, some config settings, and some doc updates.
...
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
9a8902571c
Placeholder for parallel MicroManager.
...
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
0c76a70313
Renamed traversal by "interval" to "locusWindow"
...
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
ce470702fc
consistency with java naming conventions
...
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
...
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
...
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
13d4692d2e
1. Added a by-interval traversal.
...
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
3af66a462e
Make PrintLocusContextWalker less verbose.
...
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
5abfc7d079
Added an argument ('extended' or 'ext') that outputs the four-base probs in a long format.
...
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
f2f9fa3ed4
doc added
...
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
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
...
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
24722a442e
Slight code cleanup
...
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.
...
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='.
...
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!
...
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
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.
...
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
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.
...
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
f031d882c6
ByReference traversals!
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@281 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-03 13:23:18 +00:00
93fc768c38
Fixing problems with SAMQueryIterator and reads
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@263 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 18:04:28 +00:00
bb3dbb5756
change default onTraversalDone to use the new output streams
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@249 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-01 19:50:31 +00:00
6994cca988
added precision
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@246 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-01 16:21:29 +00:00
385736469c
High performance pileup code and utilities
...
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
8d601a6a42
unbox
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@239 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-31 15:51:59 +00:00
234137dee8
use boolean instead of String for flag to suppress printing in map
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@236 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-31 15:14:00 +00:00
3896cc8f17
Moved avg depth of coverage functionality into the core depth of coverage
...
walker. Used new command line args for walkers.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@234 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-31 05:02:33 +00:00
7c6455fe36
Handle the case where a walker is being run outside of the GATK framework, such as JUnit tests.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@222 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-29 01:50:27 +00:00
d7c0bcc223
Reorganized GenomeLoc code to more clearly and better use the picard SequenceDictionary information.
...
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
cfee59e0e6
New type hierarchy for Traversals. There's a new package to hold them (traversals) and an easy system to create new ones. We are now one step closer to supporting the execution manager (a totally non-functional version is included here) that actually executes walkers in parallel using N threads.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@214 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-27 15:40:45 +00:00
4a6be896b9
Provide out and err PrintStreams to the walkers.
...
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
826781a760
The traversal engine now passes the reduce result to OnTraversalDone() in the walker base class
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@210 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-27 13:44:46 +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.
...
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
53fe9acf65
Make command-line arguments available in walker constructor, provide back door from
...
walker into GATK itself, do some cleanup of output messages, and add some bug fixes.
Command-line arguments in walkers are now feature-complete, but still a bit messy.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@203 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-26 20:45:27 +00:00
5f9010116a
Collapse the walker hierarchy, in preparation for in-walker output streams less hokey walker args.
...
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
8bdf49a01f
added slightly more useful output to Depth of Coverage walker. (now prints number of loci). Traversal engine now actually prints the reduce result (key) and no longer prints millions of locus interval updates
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@183 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-25 03:12:54 +00:00
63cd1fe201
Push core / playground lower into the tree.
...
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
hanna
ebanks
depristo
kiran
asivache
jmaguire