ed8c92a12a
make isReference do the right thing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1439 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-19 20:32:29 +00:00
21091b9839
Fix for invalid format error when outputting BAM files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1438 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-19 19:42:39 +00:00
4cf9110468
Adding a lot of changes to the VCF code, plus a new basic validator. Also removing an extra copy of the Artificial SAM generator that got checked in at some point.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1437 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-19 05:08:28 +00:00
b3fe566c0c
Fix descriptions of walker args
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1436 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-18 19:46:48 +00:00
82e2b7017e
Prevent array bounds errors
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1435 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-18 16:54:31 +00:00
26a6f816c9
set default value for output format
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1434 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-18 16:17:09 +00:00
53153fcd79
Allow RODs to specify that incomplete records are okay (i.e. that they allow optional fields)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1433 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-18 15:26:10 +00:00
9b1d7921e8
added filter based on concordance to another call set
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1432 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-18 15:16:30 +00:00
b2a18a9d61
- first pass at a basic indel filter (for now, based on size and homopolymer runs)
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- fix simple indel rod printout
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1431 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-18 03:04:12 +00:00
78439f7305
Modify Sequenom input format based on official documentation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1430 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-18 01:42:57 +00:00
63d90702d6
another iteration of the VCFReader and VCFRecord, introducing the VCFWriter
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1429 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-17 22:17:34 +00:00
1e8b97b560
quietly skip empty intervals files rather than crash.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1428 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-17 20:19:14 +00:00
92c63fb530
It's just "lod" not discovery_lod now.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1427 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-17 18:44:09 +00:00
df5744bcd3
update this walker so any variants can be passed in
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1426 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-17 16:30:39 +00:00
8403618846
the start to the VCF implementation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1425 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-17 04:34:15 +00:00
d4808433a1
Added option to output the locations of indels in the alternate reference
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1424 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-16 03:46:36 +00:00
4b6ddc55bd
Merge our 2 fastq writers into 1: incorporate Kiran's secondary-base file writer into the fasta/fastq writers
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1423 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-14 20:55:23 +00:00
0ec581080c
Refactoring the code; also, now it prints continuously instead of potentially storing one long string.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1421 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-13 01:32:46 +00:00
2a01e71277
A very simple standalone filter for fooling around with the data: can extract only mapped or only unmapped reads, only reads with mapping quals > X, reads with average base qual > Y, reads with min base qual > Z, reads with edit distance from the ref > MIN and/or < MAX
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1420 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-12 20:28:51 +00:00
ebec0ec171
A standalone companion to BamToFastqWalker: does the same thing but without calling in gatk's heavy artillery (does not "require" a reference either). Extracts seqs and quals and places them into fastq; along the way it also reverse complements reads that align to the negative strand (so that fastq contains reads as they come from the machine).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1419 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-12 20:24:37 +00:00
112a283f54
be nice, don't forget to close the reader when done
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1418 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-12 20:19:56 +00:00
ba2a3d8a58
Reverse qualities when read seq. is reverse complemented
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1417 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-12 20:17:35 +00:00
144b424933
Added : String reverse(String s) - reverses a string
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1416 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-12 20:16:22 +00:00
143f8eea4e
option to output in sequenom input format
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1415 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-12 16:50:37 +00:00
7f1159b6a9
Added option to mask out SNP sites with "N"s in the new reference.
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This is useful when producing Sequenom input files for validating indels...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1414 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-12 15:17:45 +00:00
43f63b7530
Added a walker to convert a bam file to fastq format (including the option to re-reverse the negative strand reads).
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Picard has such a tool but it is geared towards their pipeline and requires intimate knowledge of the lanes/flowcells,etc. This is just easy.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1413 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-12 15:10:40 +00:00
d101c20b30
added the ability to pass in a csv file of ROD triplets (one triplet per line) to the -B option
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1412 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-11 22:10:20 +00:00
e4acd14675
Now GenomicMap maps (and RemapAlignment outputs) regions between intervals on the master reference as 'N' cigar elements, not 'D'. 'D' is now used only for bona fide deletions.
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Also: do not die if alignment record does not have NM tags (but mapping quality will not be recomputed after remapping/reducing for the lack of required data)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1411 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-11 21:10:17 +00:00
2c3f56cb8d
fix length calculation (it was including +/- char when it shouldn't)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1410 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-11 20:28:24 +00:00
5fab934f4e
- moved the reference maker to its own directory
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- added first version of a more complicated reference maker which takes in RODs and creates an alternative reference based on the variants (indels and/or SNPs)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1409 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-11 18:01:06 +00:00
d69ae60b69
fixed two tests affected by my previous commit
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1408 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-11 17:57:50 +00:00
fc1c76f1d2
fixing a bug where reads in overlapping interval based locus traversals could get assigned to only one of two the regions
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1407 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-11 17:50:16 +00:00
1851613de4
Now using larger database of HLA alleles
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1405 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-11 03:11:14 +00:00
dd228880ed
Partially implemented NewHotnessGenotypeLikelihoodsTest caused the tests to fail.
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Ouch! So hot it burned me.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1403 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-10 20:45:44 +00:00
3208eaabcc
A standalone picard-level tool for breaking individual reads into "pairs" of first/last N bases. Supports:
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* splitting off only start or end of the read, or both; the output will contain
chopped sequences AND corresponding base qualities
* splitting arbitrary number of bases off each end (different numbers
for left and right segments can be specified; segments can overlap)
* splitting only unmapped reads, ignoring mapped ones
* writing splitted ends into separate sam/bam files, or into a single output file
* decorating original read names with user-specified suffixes for each end
(e.g. _1 and _2 for left and right parts of the read); default: no decoration,
original read names are used
* when mapped reads are split, the alignment cigars are chopped appropriately
and the alignment start positions are adjusted (for the right end) to correctly
specify the alignment of the selected part of the read
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1402 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-10 20:42:49 +00:00
36312ae4b2
tiny cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1401 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-10 20:26:52 +00:00
ecae619a1b
warn user when dbSNP rod looks suspicious
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1400 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-10 20:20:20 +00:00
2841e151d0
javadoc comments only
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1399 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-10 18:44:35 +00:00
921d4f4e95
RemapAlignments is a standalone picard-level tool that does not use gatk engine; moved to 'tools'
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1396 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-10 15:41:07 +00:00
02f1af0743
Don't die when a readgroup is absent from the covariates table - it could
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happen when all reads are unmapped (or have MQ0); instead, just don't alter
the quals.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1394 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-10 03:10:33 +00:00
089dab00e2
Was discordance rate, now concordance rate
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1393 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-07 19:37:52 +00:00
6d3ef73868
Now includes statistics on the allele agreement with dbSNP -- counts concordant calls as dbSNP = A/C and we say A/C, vs. we say A/T
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1392 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-07 19:37:07 +00:00
20baa80751
Updated polarized reference priors, need DiploidGenotypePriors class that is directly used by the NewHotness genotypelikelihoods, more bug fixes and refactoring, etc.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1391 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-07 19:01:04 +00:00
a864c2f025
Updated polarized reference priors, need DiploidGenotypePriors class that is directly used by the NewHotness genotypelikelihoods, more bug fixes and refactoring, etc.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1390 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-07 19:00:06 +00:00
db250f8d3e
Don't print if not in learning mode
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1389 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-07 06:08:02 +00:00
4c1fa52ddf
-Added mapping quality zero filter
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-Set some reasonable defaults (based on pilot2)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1388 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-07 03:18:02 +00:00
bbd7bec5db
Continuing cleanup of SSG. GenotypeLikelihoods now have extensive testing routines. DiploidGenotype supports het, homref, etc calculations. SSG has been cleaned up to remove old garbage functionality. Also now supports output to standard output by simply omitting varout
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1387 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-05 22:25:30 +00:00
d60d5aa516
Fixed bug: previously reset likelihoods after each region/exon.
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Better comments/documentation added
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1386 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-05 18:44:46 +00:00
0d47798721
made booster distance a parameter
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1385 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-05 18:29:21 +00:00
3b74b3ba74
print out ref/alt ratio, not major/minor
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1384 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-05 16:36:25 +00:00
48713e154c
Windowed access to the reference.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1383 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-05 16:29:15 +00:00
65e9dcf5b7
Fully operational version of the new genotype likelihoods class. (1) Much cleaner interface. Now explicitly stores likelihoods, priors, and posteriors in separate arrays indexed by an enum, (2) no longer can be used to make calls, it relies on SSGGenotypeCall to order the likelihoods, calculate best to ref, etc, this is just for calculating genotype likelihoods now; (3) Now performs extensive error checking with validate() to ensure the system is behaving properly. (4) fixed incorrect treatment of N bases, which we being counted against everyone (5) likely found a stats bug in which heterozyosity was being applied incorrectly to the genotype priors
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1382 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-05 01:00:55 +00:00
4dc23f2763
Trivial formatting changes as I moved more legacy code into this system
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1381 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-05 00:54:26 +00:00
34af669dbb
Explicit ENUM representation of the diploid genotypes. Please use this from now on to represent strings like AA or AT
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1380 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-05 00:53:43 +00:00
5487ab0ee6
Added several useful routines to MathUtils for summing and bounds checking of doubles
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1379 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-05 00:41:31 +00:00
68309408e4
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1378 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-04 21:23:01 +00:00
45ab212f22
Post-presentation update
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1377 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-04 21:21:12 +00:00
21d1eba502
Cleaned division of responsibilities between arguments to map function. Reference has been changed
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from an array of bases to an object (ReferenceContext), and LocusContext has been renamed to reflect
the fact that it contains contextual information only about the alignments, not the locus in general.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1376 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-04 21:01:37 +00:00
a5a7d7dab8
added "booster" metrics
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1375 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-04 20:53:45 +00:00
3a8d923785
minor output changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1374 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-04 20:12:16 +00:00
939b19e715
Committing the first version of the homopolymer filter. Removes SNPs that occur at the edges of homopolymer runs and whose nonref allele matches the repeated base in the homopolymer.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1373 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-04 14:35:51 +00:00
20ff603339
New hotness and old and Busted genotype likelihood objects are now in the code base as I work towards a bug-free SSG along with a cleaner interface to the genotype likelihood object
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1372 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-03 23:07:53 +00:00
4986b2abd6
Fixing bug in SSG -- genotyping and discovery were mixed up by name
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1371 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-03 22:13:35 +00:00
3485397483
Reorganization of the genotyping system
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1370 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-03 20:55:31 +00:00
9f1d3aed26
-Output single filtration stats file with input from all filters
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-move out isHet test to GenotypeUtils so all can use it
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1369 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-03 20:44:21 +00:00
880a01cb5d
Slight reorganization of genotype interface
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1367 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-03 19:18:41 +00:00
d840a47b11
Slight reorganization of genotype interface
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1366 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-03 19:17:15 +00:00
20986a03de
cleanup before moving files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1365 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-03 19:08:24 +00:00
e3b08f245f
Pull out RMS calculation into MathUtils for all to use
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1364 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-03 17:00:20 +00:00
e495b836d3
- added mapping quality filter
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- make the filters brainless in that they strictly have thresholds and filter based on them; require user to calculate and input these thresholds.
- update filters in preparation for migration to new output format
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1363 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-03 16:46:51 +00:00
ba07f057ac
finish the math for RMS
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1362 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-03 16:18:09 +00:00
8bc925a216
Commit on the behalf of Mark: cleaning up some old and busted code in GenotypeLikelihood and associated objects.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1361 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-31 21:18:30 +00:00
9dfee7a75c
the "-genotype" option now acts correctly as a discovery mode caller in SSG
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1359 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-31 18:31:45 +00:00
c2c80dd946
cleanup and moving some things around to more logical locations
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1358 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-31 16:28:39 +00:00
9dada95ec3
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1357 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-31 16:21:16 +00:00
9a0761cd8f
accidentally committed some debug code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1356 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-31 15:25:22 +00:00
2f2c8576a5
GLF output is now well validated, and some changes for new Genotypes interface code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1355 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-31 15:21:28 +00:00
8eeb87af2a
Tests for downsampling related utilities in ListUtils class that didn't get checked in earlier
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1352 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-31 00:09:35 +00:00
678c2533ca
Removed custom output stream for file and replaced with the standard out PrintStream
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1350 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-30 22:36:42 +00:00
2a7dfce9ae
fix the header string mismatch that Andrew found
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1349 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-30 22:26:34 +00:00
44673b2dce
Removed a debugging println that was accidentally checked in
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1348 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-30 22:23:27 +00:00
845488ff94
VariantEval now decides whether a variant is not confidently called using BestVsNetxBest if genotypes are being evaluated and BestVsRef if not (variant discovery only). Also, the absolute value of the BestVsRef LOD (getVariantionConfidence) is used so that confident reference calls (if the GELI has output them) will show up in the final table as reference calls rather than no calls.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1347 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-30 21:54:06 +00:00
fdc7cc555b
Removed extra column name from geliHeaderString that was mislabeling the 10 genotype likelihoods by shifting them over by onex
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1345 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-30 21:42:02 +00:00
0087234ed7
small code cleanup, a couple of little changes to SSGGenotypeCall
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1343 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-30 19:47:37 +00:00
fbc7d44bc7
don't allow users to input priors anymore; they should be using heterozygosity and having the SSG calculate priors.
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Note that nothing was changed for dnSNP/hapmap priors (not sure what we want to do with these yet - any thoughts?)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1342 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-30 19:10:33 +00:00
b282635b05
Complete reworking of Fisher's exact test for strand bias:
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- fixed math bug (pValue needs to be initialized to pCutoff, not 0)
- perform factorial calculations in log space so that huge numbers don't explode
- cache factorial calculations so that each value needs to be computed just once for any given instance of the filter
I've tested it against R and it has held up so far...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1341 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-30 18:52:13 +00:00
4033c718d2
moving some code around for better organizations, some fixes to the fields out of SSG
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1340 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-30 15:09:43 +00:00
4366ce16e0
Made sure all RODs have a (good) toString() method - and use it in the Venn walker. (thanks, Mark)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1339 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-30 14:53:27 +00:00
9cd53d3273
some initial changes from the first review of the genotype redesign, more to come.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1338 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-30 07:04:05 +00:00
feb7238f10
Wasn't always returning the correct alt base
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1337 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-30 03:08:04 +00:00
5429b4d4a8
A bit of reorganization to help with more flexible output streams. Pushed construction of data
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sources and post-construction validation back into the GATKEngine, leaving the MicroScheduler
to just microschedule.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1336 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-29 23:00:15 +00:00
bca894ebce
Adding the intial changes for the new Genotyping interface. The bullet points are:
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- SSG is much simpler now
- GeliText has been added as a GenotypeWriter
- AlleleFrequencyWalker will be deleted when I untangle the AlleleMetric's dependance on it
- GenotypeLikelihoods now implements GenotypeGenerator, but could still use cleanup
There is still a lot more work to do, but this is a good initial check-in.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1335 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-29 19:43:59 +00:00
c5c11d5d1c
First attempt at modifying the VFW interfaces to support direct emission of relevant training data per feature and exclusion criterion. This way, you could run the program once, get the training sets, and then feed that training set back to the filters and have them automatically choose the optimal thresholds for themselves. This current version is pretty ugly right now...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1334 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-29 19:29:03 +00:00
3554897222
allow filters to specify whether they want to work with mapping quality zero reads; the VariantFiltrationWalker passes in the appropriate contextual reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1333 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-29 17:38:15 +00:00
7a13647c35
Support for specifying SAMFileReaders and SAMFileWriters as @Arguments directly. *Very*
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rough initial implementation, but should provide enough support so that people can stop
creating SAMFileWriters in reduceInit.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1332 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-29 16:11:45 +00:00
56f769f2ce
Output improvements to GenotypeConcordance calculations
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1331 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-29 12:54:46 +00:00
72dda0b85c
Fixed calculations for Mark
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1330 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-29 03:21:43 +00:00
f0378db9b7
added accuracy numbers
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1329 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-29 01:38:33 +00:00
a5a56f1315
At this point, we are convinced that the new priors are the way to go...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1328 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-28 17:25:25 +00:00
df4fd498c5
Improvements and bug fixes galore. (1) Now properly handles Q0 bases, filtering them out, you can disable this if you need to (2) support for three-state base probabilities (see email), which is disabled by default (still experimental) but appears to be more emppowered to detect variants (see email too)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1327 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-28 13:21:38 +00:00
46643d3724
Improvements and bug fixes galore. (1) Now properly handles Q0 bases, filtering them out, you can disable this if you need to (2) support for three-state base probabilities (see email), which is disabled by default (still experimental) but appears to be more emppowered to detect variants (see email too)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1326 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-28 13:21:27 +00:00
3c4410f104
-add basic indel metrics to variant eval
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-variants need a length method (can't assume it's a SNP)!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1324 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-28 03:25:03 +00:00
1d6d99ed9c
walk by reference
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1323 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-27 20:21:04 +00:00
089ae85be7
1. output grep-able strings for genotype eval
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2. free DB coverage from isSNP restriction
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1322 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-27 17:36:59 +00:00
1bca9409a4
calculate freestanding intervals
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1321 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-27 16:40:27 +00:00
2499c09256
added minIndelCount (short: minCnt) command line argument. The call is made only if the number of reads supporting the consensus indel is equal or greater than the specified value (default: 0, so only minFraction filter is on in default runs!)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1320 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-27 15:22:51 +00:00
73ddf21bb7
SNPs no longer fail this filter if they are actually hom in reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1319 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-27 15:20:43 +00:00
f2b3fa83ac
fix for another bug found by Eric: some indels were printed into the output stream twice (when there's another indel within MISMATCH_WINDOW bases and that other indel requires delayed print in order to accumulate coverage)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1318 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-27 15:07:07 +00:00
f1109e9070
Added the interator to SAMDataSource to prevent seeing dupplicate reads, only in a byReads traversal. The iterator discards any reads in the current interval that would have been seen in the previous interval.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1317 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-25 22:36:29 +00:00
5eca4c353c
IndelGenotyper now uses GATK::getMergedReadGroupsByReaders() to sort out which read in the merged stream is for normal, and which is for tumor (in --somatic mode, apparently)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1316 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-24 23:01:18 +00:00
a361e7b342
SAMDataSource is now exposed by GATK engine; SamFileHeaderMerger is exposed from Resources all the way up to SAMDataSource, so now we can see underlying individual readers should we need them; GATK engine has new methods getSamplesByReaders(), getLibrariesByReaders(), and getMergedReadGroupsByReaders(): each of these methods returns a list of sets, with each element (set) holding, respectively, samples, libraries, or (merged) read groups coming from an individual input bam file (so now when using multiple -I options we can still find out which of the input bams each read comes from)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1315 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-24 22:59:49 +00:00
2024fb3e32
Better division of responsibilities between sources and type descriptors.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1314 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-24 22:15:57 +00:00
64221907a2
fixed a bug found by Eric: genotyper would crash in the case of an indel too close to the window end, with the next read mapping sufficiently far away on the ref
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1313 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-24 21:00:31 +00:00
2db86b7829
Move the cleaned read injector test from playground to core. Remove CovariateCounterTest's dependency on the CleanedReadInjector. Start doing a bit of cleanup on the CLP's FieldParsers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1312 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-24 19:44:04 +00:00
df44bdce7d
Retire the pooled caller...its been eclipsed by other walkers in the tree.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1310 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-24 14:49:03 +00:00
884806fc16
Broken and unused. It goes away now.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1309 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-24 14:26:52 +00:00
d044681fbe
change paths to new ones
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1308 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-24 07:28:43 +00:00
59f0c00d77
-set indel cleaning walkers to be in core package
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-move Andrey's alignment utility classes to core
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1307 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-24 05:23:29 +00:00
bb20462a7c
A better way: down-scale second-base ratios until the infinities disappear. This way, high-coverage sites don't cause binomialProbability to explode.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1306 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-24 03:02:00 +00:00
0b16253db3
an iterator to fix the problem where read-based interval traversals are getting duplicate reads because reads span the two intervals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1305 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-23 23:59:48 +00:00
7c20be157c
Added ability to sample from a list *without* replacement.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1304 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-23 21:00:19 +00:00
038cbcf80e
If the result from the secondary-base test is 0.0, replace the result with a minimum likelihood such that the log-likelihood doesn't underflow.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1303 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-23 20:59:52 +00:00
093550a3f2
Removed secondary-base test from SingleSampleGenotyper. It now lives in the variant filtration system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1302 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-23 20:58:41 +00:00
477502338f
moved major indel cleaning pieces to core (yippee!)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1301 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-23 19:59:51 +00:00
4efe26c59a
Major: allow genotyper to optionally output in 1KG format, including outputting the samples in which indels are found.
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Minor: refactor 454 filtering
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1300 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-23 19:53:51 +00:00
f8b1dbe3b3
getBestGenotype() does not necessarily return hets in alphabetical order;
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the string (unfortunately) needs to be sorted for lookup in the table (otherwise we throw a NullPointerException)
TO DO: have the table be smarter instead of sorting each genotype string
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1298 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-23 01:58:47 +00:00
ee8ed534e0
print full genotype for alt allele
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1297 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-23 01:35:23 +00:00
298cc24524
Fix minor bug introduced in filtration, and cleaned up the artificial sam records so that they use SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX and SAMRecord.NO_ALIGNMENT_START rather than hardcoded -1's.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1296 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-22 22:37:41 +00:00
cac04a407a
For Manny: filter out reads where the the ref index ==
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NO_ALIGNMENT_REFERENCE_INDEX but the alignment start != NO_ALIGNMENT_START.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1295 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-22 21:19:24 +00:00
9c12c02768
AlleleBalance and on/off primary base filters -- version 0.0.1 -- for experimental use only
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1294 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-22 17:54:44 +00:00
c54fd1da09
Beautify the genotype concordance printouts
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1291 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-22 02:53:02 +00:00
6e4fd8db4a
Better formatting of available walkers, and only output them along with help. Cleanup JVMUtils.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1290 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-21 22:23:28 +00:00
761d70faa1
Better printing of multiple rods -- now produces a comma-separated set of values
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1289 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-21 21:58:27 +00:00
8588f75eb6
Better printing with toSimpleString() -- now prints out chip-genotype string
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1288 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-21 21:57:59 +00:00
1843684cd2
Cleanup: GATKEngine no longer needs to be lazy loaded, b/c the plugin directory no longer exists.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1287 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-21 18:50:51 +00:00
b43925c01e
Switched to Reflections ( http://code.google.com/p/reflections/ ) project for
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inspecting the source tree and loading walkers, rather than trying to roll
our own by hand.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1286 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-21 18:32:22 +00:00
436a196e2b
Bug fixes to support hapmap genotyping concordance.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1285 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-21 16:20:10 +00:00
7e04313b4e
Bug fixes and improvements to CoverageHistogram. Now displays the frequency of the bin. Also correctly prints out the last element in the coverage histogram (<= vs. <)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1284 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-21 11:55:05 +00:00
f13a1e8591
adding a couple of small changes to support contract with VariantEval
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1283 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-21 03:49:15 +00:00
b4adb5133a
GLF rod as a AllelicVariant object.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1282 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-21 00:55:52 +00:00
f314ef8d84
Features and exclusion criteria are now instantiated in VariantFiltrationWalker's initialize() method, rather than in every map() call. This means the features and exclusion criteria will only ever be initialized once.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1281 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-20 22:47:21 +00:00
54fce98056
duh, don't print newline
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1280 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-20 03:04:27 +00:00
1d2b545608
add FLT toString method (to be used in PrintRODs) and add it to ROD list
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1279 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-20 02:47:50 +00:00
8da754eb4e
First implementation of a primary base filter. Assumes distribution of on/off bases is distributed according to a binomial.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1278 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-17 18:43:35 +00:00
24ebfee604
don't print traversal stats
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1277 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-17 16:13:28 +00:00
387316ebe1
added indel rod
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1276 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-17 16:05:51 +00:00
da4af3b620
print indels in the format required for 1KG submissions
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1275 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-17 15:59:18 +00:00
d45c90b166
ROD to represent simple output from IndelGenotyper
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1274 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-17 14:36:12 +00:00
f978b04633
A very simple walker to print out (using the ROD's toString method) all of
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the RODs it sees. This is the easiest solution to get around the (temporary)
bug of reads being seen multiple times by reads walkers when close intervals
are passed to them (i.e. process full contigs and then use a ref walker to
filter the ones within your intervals of choice)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1273 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-17 14:03:34 +00:00
129ad97ce5
performance improvement to GenomeLocParser -- moved regex pattern compile out of local field
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1272 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-17 02:56:25 +00:00
ebanks
hanna
aaron
jmaguire
asivache
sjia
depristo
kcibul
mmelgar
kiran
andrewk