9bd6489f8e
Output indels in the format appropriate for low-coverage indel submission
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@832 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 17:32:15 +00:00
919e995b7f
-Moved my walkers to indels directory
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-Removed entropy walker and replaced it with mismatch (column) walker
-Some improvements to the cleaner (more to come)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@830 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 16:34:24 +00:00
b81135c606
bug fixed; this rod seems to work now...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@826 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 22:25:34 +00:00
ab7bb5800a
forgot to remove debug print statement
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@823 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 21:38:27 +00:00
568a0d3c27
exon coordinates are now parsed correctly (?). IF DELIMITER IS THE LAST CHARACTER IN A STRING, String.split() DOES NOT return empty field as the last one; instead, the last field returned will be the one immediately before such delimiter! Wicked.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@822 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 21:36:50 +00:00
f4119c17de
still working on it...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@821 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 21:07:38 +00:00
23b7a28015
simple walker that works off pre-computed tumor/normal genotyping calls (e.g. samtools pileup). Collects overal stats and also writes somatic variants into IGV-compatible bed file if asked to. NOT finished. NOT tested
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@819 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 21:05:47 +00:00
8f1cabd33d
cmd line args changed - again; internally uses VariantType enum
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@818 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 21:03:58 +00:00
4edcdffe45
refseq annotation track: should be able to provide (multiple) transcript annotations available over a given genomic position. NOT finished and NOT tested!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@815 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 20:07:15 +00:00
149cc9989b
spaces!!!!!!!!!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@814 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 19:40:25 +00:00
c2df35b7fe
- get leftmost position of indel correct
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- don't try to clean reads with mapping quality of 0
- un-deprecate
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@813 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 17:24:58 +00:00
02fc4f145f
refactoring: a couple of general purpose (hopefully useful?) methods/classes extracted into a standalone utils class
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@802 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 18:54:40 +00:00
4b718688d5
no changes, really, just synchronizing (instead of reversing) to increase the amount of entropy
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@801 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:27:28 +00:00
893f1b6427
updated
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@800 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:25:50 +00:00
a9dfbfb309
internal changes and some refactoring. slightly different final report. Now can take tracks that implement either Genotype or GenotypeList; takes an arg specifying what variants to look for (POINT - aka snp - or INDEL); takes an arg specifying whether default ref/ref call of one type (INDEL/POINT) should be implicitly assumed if another call (POINT/INDEL respectively) was made at the same position [this is probably most useful for indels and only (?) for sam pileups: if we have only point mutation call at a given position, it does mean that we do have coverage, and that there was no evidence whatsoever for an indel, so we have an implicit 'no-indel' call]
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@799 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:25:09 +00:00
d9fc84f1e3
actually checking in the first pass
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@795 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:13:27 +00:00
7a979859a9
Intermediate checking for evaluation -- now supports transition / transversion evaluation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@793 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:05:06 +00:00
9902ce8073
properly flush the gzip output stream. this was a subtle inheritance bug.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@791 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 13:57:58 +00:00
63caca31bf
minor update in report printout format
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@790 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 13:56:09 +00:00
7afc10fd6f
updated, reports more stuff now, including stats for external consistency checks
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@789 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 22:28:18 +00:00
30c63daf89
More improvements to the duplicate quality combiner, making progress towards a clean system
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@788 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 22:26:57 +00:00
b5ad5176f7
stick headers on the output tables
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@782 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 20:35:50 +00:00
0d58e4ccc9
-check original alignments for indels when computing mismatch score
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-move logging to debug
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@778 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 19:55:42 +00:00
e6200fe5b5
don't ignore reads when maxReadLength isn't set
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also, print out LOD score for cleaning
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@771 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 19:24:10 +00:00
0219d33e10
QualityUtils: added reverse function to reverse an array of bytes (and not complement it), BaseUtils: split qualToProb into itself and qualToErrProb, CovariateCounterWalker and LogisticRecalibrationWalker: several changes including a properly acocunting (only partly complete) for reversing AND complementing bases that are negative strand, PrintReadsWalker: created option to output reads to a BAM file rather than just to the sceern (useful for creating a downsampled BAM file)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@770 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 18:30:45 +00:00
7e77c62b49
auxiliary class, a simple struct to keep together info like numbers of covered, assessed, ref/variant bases across the sample
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@769 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 16:30:16 +00:00
34f9820299
update mapping quality score and edit distance attribute for reads when they are cleaned
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@763 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 17:51:31 +00:00
01a3cb27c7
@Required / @Allows flags for main arguments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@751 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-19 23:26:17 +00:00
3441795d9c
better handling of edge cases (zero coverage, reference mistakes, etc.)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@747 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-18 18:04:37 +00:00
a39c8839c8
print percentage sign!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@745 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-18 14:38:20 +00:00
94e324b844
Write N for the alt allele when we're hom-ref.
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Stop EM loop when we've converged (likelihood[t-1] == likelihood[t]).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@737 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 13:58:11 +00:00
bd53bc18f9
added new required annotations
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@736 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 12:24:06 +00:00
81fac73c01
LOD checks for normal and brute force versions
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@732 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 02:56:03 +00:00
527df6e57b
Massive speed-up, clean-up and tabular output.
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This program is going to rule.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@731 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-16 16:52:40 +00:00
3b57a35009
don't be tricked by multiple read groups with the same sample id!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@730 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-16 15:28:55 +00:00
947bac5cdc
vast speedup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@729 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-16 15:27:58 +00:00
f33f3c0434
added LOD threshold for determining when to clean
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@725 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-15 20:23:59 +00:00
d1f3000afa
bed-style output for IGV
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@721 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-15 17:58:44 +00:00
641afc4e76
fix a crash in the event that the input file has no read groups!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@714 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 19:27:41 +00:00
7a1f85ff86
option to print out the indels found by the cleaner to a file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@709 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 17:50:08 +00:00
5dda448ae0
1. Add printouts for the cleaner
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2. First pass at the entropy interval walker (still needs work)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@696 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 13:59:48 +00:00
7b59f63f12
and don't forget to close sam writer after we are done...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@692 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-13 20:46:36 +00:00
de0cce87ea
new optional arg added that allows to specify a separate bam file to send all piles that fail to realign to; plus minor fixes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@691 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-13 20:24:23 +00:00
7084ecdeb6
a few changes; checked in to allow debugging.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@688 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-13 15:50:48 +00:00
4e4767e5de
Moved to org.broadinstitute.sting.secondarybase
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@682 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 20:26:43 +00:00
219eb60716
Added newly-required documentation to arguments so that build can complete successfully.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@681 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 20:26:10 +00:00
688358190c
Moved secondary base stuff out of playground for the purpose of making it a core utility. Modified package names and imports such that things would build properly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@680 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 20:24:18 +00:00
8079acb1d3
basic step0 implementation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@679 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 19:49:39 +00:00
57ecb7fbf1
Nicer reporting functions.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@678 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 19:48:30 +00:00
ee99320c83
Removed at Mark's request.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@677 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 19:48:21 +00:00
ebanks
asivache
andrewk
depristo
jmaguire
hanna
kcibul
kiran