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227 Commits (887adcfc7fbeb54cd386880fe810f5b62eed6d47)

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
asivache 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... 
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
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
jmaguire 6652f13a17 more verbose gff output! 
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
hanna cf929a8275 Get rid of test case's dependence on transient methods. 
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
jmaguire 6e180ed44e Unified caller is go. 
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
jmaguire f39092526d Added function RandomSubset 
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
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
kiran 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. 
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
kiran 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. 
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
kiran 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. 
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
kiran 35fc002d5d Debugging information is now written in such a way to make it easier to import into R. 
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
kiran 6ee4fe5a20 Fixed a Bustard/Firecrest file synchronization bug. 
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
kiran 817278be46 If a SAMRecord is on the negative strand, reverse complement the SQ tag. 
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
kiran 1d5a22cacf Extracts a Fastq file and the SQ tags to a separate file. 
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
kiran e410c005c0 A debugging tool to ensure the SQ tag in a four-prob SAM file matches the SAMRecord strand orientation. 
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
hanna 9c37400c4f Added basic performance testing so I can make sure concurrent access doesn't slow down overall fasta access. 
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
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 49fd951d8c Initial test suite for FastaSequenceFile2, so I can add parallelism support with abandon. 
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
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
kiran 2b59110dca CombineSamAndFourProbs is better. 
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
kiran 56aa98ad30 Ignore null values. 
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
kiran 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. 
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
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
kiran f5cc2d8b0b Commented out import of IlluminaParser. 
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
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
kiran c5220c0822 Four-base probs are now decoded with the relevant method in QualityUtils 
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
kiran 9bc763a835 A better (aka 'working') tool for combining four-base probs with an aligned sam file. 
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
kiran b7a2e82b46 Can optionally process raw or corrected intensities. 
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
kiran 6cdad10dd1 Make output type identical to the bustard parser so the values can be easily swapped for one another. 
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
kiran d0ce56e018 Remember to take the strand flag into account when calculating error rate per cycle as a surrogate for instrument performance. 
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
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
kcibul c556a97f17 Skeleton of Somatic Coverage tool 
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
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
kiran 089bf30cf4 Send things to the out file via the logger. 
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
kiran 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. 
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
kiran 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. 
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
kiran 0e7d962eca Oops. Slight twiddle of the math here so that I'm not asking if bestBase == nextBestBase. 
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
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