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237 Commits (998fad76c6a3f1af73f75cb63a744619d7573d18)

Author SHA1 Message Date
kiran 998fad76c6 Some utility methods for creating pileups of secondary bases and secondary quals. 
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
depristo 8b2c2e677b Uses the cleaner new GenomeLoc(read) syntax 
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
depristo 1cee7948ab Added lots of assertions to check for problems. 
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
depristo 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
depristo cc75e8f712 Uses the cleaner new GenomeLoc(read) syntax 
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
depristo 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 
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
depristo bb666ce392 Added mappingQualPileup function for use in the verbose mode of Pileup 
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
asivache 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 
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
asivache 8e6093d5a5 remove mom/dad/kid cmd line arguments that were needed for mendelian walker; now we can use generic track binding!! 
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
kiran 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. 
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
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