zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
382 Commits
1 Branch
0 Tags
257 MiB
Commit Graph

99 Commits (f838a5e51175224e4494da2f76c1f092467962fd)

Author SHA1 Message Date
aaron 887adcfc7f Some minor fixes to the last check-in 
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
aaron f2d0d73309 removed old shard strategy code 
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
aaron dd604799dc Added some new code for shard support over reads 
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
hanna 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
asivache 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 
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
kiran 756e6c61d8 Strictness args are presented as lowercase in the help, but only accepted if uppercase. Changed help to list the valid arguments in uppercase. 
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
kcibul c7777d46d6 * re-enabled setting of sequence dictionary information on GenomeLoc 
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
kcibul ce72932a45 * refactored GenomeLoc to use contigIndex internally for performance and fixed several calling classes 
* 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
hanna 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. 
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
hanna c2669021b8 Cleanup, and support either by-interval traversals or full traversals in data source-backed code. 
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
hanna 2322bb7d86 Workaround: use a single ReferenceIterator for an entire micromanaged traversal. We'll have to 
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
hanna 95753e1b34 Should've been calling queryOverlapping in locus mode. 
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
depristo 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 
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
hanna 0d825ccfc1 Oops. Fixed duplicate reference to the reference. 
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
aaron 9afa101465 Add interval support to the 
.__            __    __                
  _____|  |__ _____ _/  |__/  |_  ___________ 
 /  ___/  |  \\__  \\   __\   __\/ __ \_  __ \
 \___ \|   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
hanna 8a1207e4db Bringing up scaffolding for integration of locus traversals by reference with Aaron's data source code. 
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
aaron 8e2f5471a1 Some cleanup to the data source, and another JUnit test case. 
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
aaron d56193b6df Cleanup of a couple of output statements 
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
aaron 12752cf893 Added a bunch of fixes: MSRI wasn't working, sharding had broken edge cases, and SAMBAM DS needed to close the file handles. 
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
aaron d4ab95c098 Added a constructor, took out a copy constructor, and changed some SAMBAM code. 
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
kcibul 0b81a76420 added support for Picard IntervalList files to --interval_file 
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
aaron 295c269a64 Remove the main() I put in for debugging 
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
aaron d517245beb Fixes for shattering, added JUnit test case 
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
asivache 453d13415d count variant as biallelic if it's just a non-ref homogeneous site! 
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
depristo b49f713336 Enabled multiple argument for GATK driver; first step towards generalized -rods <name> <type> <file> argument structure 
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
asivache 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 
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
asivache 8ec427ab66 latest version... still under dev/testing 
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
depristo 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. 
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
asivache 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) 
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
aaron 2663ac3e4a documentation fix 
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
aaron 8a357a88a2 right...exponential should be exponential, so I might want to increment the exponent 
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
aaron 6ce9e0f941 delete the old strategy 
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
aaron 08fddd43af -Replaced adaptive and linear strategies with an adaptive linear strategy 
-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
aaron 6369d23b43 renamed; these files are more strategy than actual shards 
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
asivache e95f427965 Added isReference() to AllelicVariant and updated rodDbSNP accordingly 
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
aaron 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. 
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
aaron 150bca30aa typO in the documentation... 
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
aaron 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 
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
aaron 0fc8a90553 removing some files from the old approach to dataSource 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@303 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-06 21:57:34 +00:00
aaron 5feb7ee627 temperary fix, relying on a old reference order data constructor 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@302 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-06 21:38:41 +00:00
aaron af5a443e5a add Synchronized to the has_next and next methods 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@301 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-06 21:17:11 +00:00
aaron 97d14abe85 Interface check-in for Matt 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@300 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-06 21:14:19 +00:00
asivache 0d25e71953 a declaration is made generic 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@295 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-04 21:55:02 +00:00
asivache 551ce9130f added isBiallelic() to the AllelicVariant interface and to rodDbSNP implementation. We probably don't really know how to deal with non-biallelic sites just as yet... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@294 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-04 21:31:16 +00:00
depristo 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
ebanks 42eb356782 1. modifed by read traversals with indexes to be more general 
2. GenomeLocs for reads should have ends spanning the read
   (moved it to GenomeLoc from Utils)
3. Got rid of those stupid unmappable characters from comments in various files


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@289 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-03 18:24:08 +00:00
andrewk 86fc18e9fc Fixed merge bug 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@288 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-03 17:41:58 +00:00
andrewk bef475778f - Updated --hapmap switch to --hapmap-chip to reflect the data being chip data for an individual rather than population allele frequency data in Hapmap 
- Corrected some bugs to get metrics logging working
- Added a switch --force_1base_probs to ignore 4-base probalities if they exist


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@287 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-03 17:32:31 +00:00
depristo edc44807af rod's now have names. Use getName() to access it. Next step is better interface to accessing rods 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@286 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-03 16:41:33 +00:00
depristo 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