f0179109fa
Removing min confidence for on/off genotype
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1473 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-28 01:04:13 +00:00
dc9d40eb9a
Now requires a minimum genotype LOD before applying tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1471 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-28 00:19:23 +00:00
a639459112
Trival consistency change from char in to char out, not char in to byte out
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1466 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-27 23:37:37 +00:00
6012f7602b
@ minor fixes to CoverageAndPowerWalker and AnalyzePowerWalker (switching to By Reference traversal, spitting out Syzygy position for sanity check)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1465 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-27 21:44:18 +00:00
bd1e679bc5
@ Fixed issues with AnalyzePowerWalker which depended on CoverageAndPowerWalker. The latter was changed but not the former. Now fixed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1464 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-27 20:23:41 +00:00
a17dad5fa9
Converts from fastq.gz to unaligned BAM format. Accepts a single fastq (for single-end run) or two fastqs (for paired-end run). Also allows you to set certain BAM metadata (read groups, etc.).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1463 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-27 20:20:09 +00:00
8740124cda
@ListUtils - Bugfix in getQScoreOrderStatistic: method would attempt to access an empty list fed into it. Now it checks for null pointers and returns 0.
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@MathUtils - added a new method: cumBinomialProbLog which calculates a cumulant from any start point to any end point using the BinomProbabilityLog calculation.
@PoolUtils - added a new utility class specifically for items related to pooled sequencing. A major part of the power calculation is now to calculate powers
independently by read direction. The only method in this class (currently) takes your reads and offsets, and splits them into two groups
by read direction.
@CoverageAndPowerWalker - completely rewritten to split coverage, median qualities, and power by read direction. Makes use of cumBinomialProbLog rather than
doing that calculation within the object itself.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1462 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-27 19:31:53 +00:00
1da45cffb3
New:
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Minor changes to CoverageAndPowerWalker bootstrapping (faster selection of indeces).
Entirely new Aritifical Pool Walker (ArtificialPoolWalkerMk2), will likely replace ArtificialPoolWalker on the next commit. Adapted the method of sampling, and added a helper context class: ArtificialPoolContext which carries much of the burden of calculation and data handling for the walker. The walker itself maps and reduces ArtificialPoolContexts.
Cheers!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1461 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-26 21:42:35 +00:00
92ea947c33
Added binomProbabilityLog(int k, int n, double p) to MathUtils:
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binomialProbabilityLog uses a log-space calculation of the
binomial pmf to avoid the coefficient blowing up and thus
returning Infinity or NaN (or in some very strange cases
-Infinity). The log calculation compares very well, it seems
with our current method. It's in MathUtils but could stand
testing against rigorous truth data before becoming standard.
Added median calculator functions to ListUtils
getQScoreMedian is a new utility I wrote that given reads and
offsets will find the median Q score. While I was at it, I wrote
a similar method, getMedian, which will return the median of any
list of Comparables, independent of initial order. These are in
ListUtils.
Added a new poolseq directory and three walkers
CoverageAndPowerWalker is built on top of the PrintCoverage walker
and prints out the power to detect a mutant allele in a pool of
2*(number of individuals in the pool) alleles. It can be flagged
either to do this by boostrapping, or by pure math with a
probability of error based on the median Q-score. This walker
compiles, runs, and gives quite reasonable outputs that compare
visually well to the power calculation computed by Syzygy.
ArtificialPoolWalker is designed to take multiple single-sample
.bam files and create a (random) artificial pool. The coverage of
that pool is a user-defined proportion of the total coverage over
all of the input files. The output is not only a new .bam file,
but also an auxiliary file that has for each locus, the genotype
of the individuals, the confidence of that call, and that person's
representation in the artificial pool .bam at that locus. This
walker compiles and, uhh, looks pretty. Needs some testing.
AnalyzePowerWalker extends CoverageAndPowerWalker so that it can read previous power
calcuations (e.g. from Syzygy) and print them to the output file as well for direct
downstream comparisons.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1460 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-25 21:27:50 +00:00
478f426727
Fixed a missing method implementation in these two files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1459 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-25 21:21:58 +00:00
f12ea3a27e
Added ability for all filters to return a probability for a given variant - interpreted as the probability that the given variant should be included in the final set. The joint probability of all the filters is computed to determine whether a variant should stay or go. At the moment, this is only visible in verbose mode (specify -V). Also removed 'learning mode'; now, filters emit important stats no matter what. Various code cleanups.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1458 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-25 21:17:56 +00:00
0bdecd8651
A most stupid bug. In cases when more than one indel variant was present in cleaned bam file, the "consensus" (max. # of occurences) call was computed incorrectly, and most of the times the call itself was not made at all. Fortunately, the locations where we see multiple indels are a minority, and many of them are suspicious anyway (manifestation of alignment problems?). Could change results of POOLED calls though.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1448 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-20 22:31:44 +00:00
6c0adc9145
resuse fasta file reader
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1446 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-20 16:01:58 +00:00
10c98c418b
Walker to determine the concordance of 2 genotype call sets.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1443 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-20 01:32:44 +00:00
1d74143ef4
A convenience argument - for Mark - so that you don't have to specify all the output file names
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1442 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-20 00:49:12 +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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
df1c61e049
Re-add the plugin path.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1271 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-16 22:48:44 +00:00
7c30c30d26
Cleaned up some duplicate code in preparation for making plugin dir configurable.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1270 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-16 22:02:21 +00:00
31f3f466ca
Improvements to support GLF generation -- now correctly handles GLF
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1269 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-16 21:10:39 +00:00
0548026a2e
Now understanding GLFs for calculating genotyping results like callable bases, as well as avoids emitting stupid amounts of data when doing a genotype evaluation (i.e., ignores non-SNP() calls)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1267 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-16 21:03:26 +00:00
c5f6ab3dd5
CoverageHistogram now sees 0 coverage sites
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1266 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-16 20:58:41 +00:00
8bc0832215
Generate chip concordance table.
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This should work, although I need to test it with some real GLFs
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1265 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-16 17:44:47 +00:00
e1055bcc4c
moving to new external repository
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1261 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-15 20:46:08 +00:00
4a730adfc1
committing latest changes before moving repositories
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1260 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-15 20:44:02 +00:00
a245ee32fa
A walker to split 2 call sets into their intersection/union/disjoint (sub)sets.
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Yes, the name is retarded, but I'm under pressure here...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1258 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-15 20:20:47 +00:00
00d49976fb
committing latest changes before moving repositories
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1255 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-15 18:41:52 +00:00
9ecb3e0015
adding GLFRods with tests and some other code changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1251 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-15 15:30:19 +00:00
c25f84a01c
Regression: we lost our hack to work around BAM files with index problems (affects BAM files created before 23 Apr 2009 and traversed by interval). Added the hack back in, along with a much more explicit comment about why its there.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1248 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-15 14:41:37 +00:00
1798aff01b
VariantEval now understands the difference between a population-level analysis and a genotype analysis, and handles both. All analyses annotated as supporting one or the other or both. Preparation for genotype chip concordance calculations as well as called sites, etc analyses
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1247 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-15 14:07:13 +00:00
84d407ff3f
Fixing odd merge problem with VariantEval -- better cluster analysis (no cumsum), rodVariant is now an AllelicVariant
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1239 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-14 18:53:27 +00:00
7d755a4c90
GenotypeLikelihoods doesn't emit metrics, they don't make sense
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1236 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-14 17:22:28 +00:00
01fc8da270
adding the GenotypeLikelihoodsWalker, which generates GLF genotype likelihoods that are pretty much identical to the samtools calls.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1235 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-14 16:57:18 +00:00
36819ed908
Initial changes to the SSG to output GLF by default
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1231 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-14 08:46:04 +00:00
a1d33f8791
-Added walker to dump strand test results to file
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-Refactored strand filter to handle calls from the walker
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1229 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-14 01:56:50 +00:00
52659d02d4
ignore unmapped reads in all the indel walkers (since they're giving me overhead issues)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1224 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-13 16:51:11 +00:00
4c02607297
genotyper also needs to have 454 reads filtered out
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1221 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-10 23:19:28 +00:00
dea72c576e
use the filter to ignore 454 reads in the traversal to speed up cleaning
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(since there's less area to actually clean against)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1220 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-10 18:34:44 +00:00
1401606344
move warning about strictly adjacent intervals in a contig from 'remap' to 'read', so it is issued only once
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1218 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-10 17:58:11 +00:00
e01d37024a
now updates mapping quality (to an arbitrary chosen value of 37 if the resulting mapping is unique) and X0, X1 tags after remapping (in REDUCE mode)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1216 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-10 16:40:52 +00:00
03e1713988
Better support for specifying read filters to apply directly from the walkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1212 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-09 23:59:53 +00:00
d86717db93
Refactoring of the traversal engine base class, I removed a lot of old code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1209 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-09 21:57:00 +00:00
bc44e08225
refactored output logic
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1204 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-09 16:13:01 +00:00
3fe7104963
Added walker to filter out clustered SNPs from a call set
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1203 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-09 03:16:27 +00:00
c8fcecbc6f
Added ParseDCCSequenceData.py to repository and made changes that allow an analysis of quantity of sequence data by platform and project, moved table / record system to a new module called FlatFileTable.py and built that into ParseDCCSequenceData and CoverageEval.py; changed lod threshold in CoverageEvalWalker.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1201 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 22:04:26 +00:00
433ad1f060
Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1196 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 18:49:08 +00:00
0a67386525
.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1195 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 16:59:36 +00:00
c78a72e775
Applies Fisher's Exact Test to determine whether there's a strand bias and, if so, filters the call out.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1193 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 16:14:11 +00:00
b211f500a3
Applies secondary base feature to variants.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1192 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 16:13:29 +00:00
6e31057e6b
Some changes involving output of marginal calls to different, per-filter files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1191 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 16:12:57 +00:00
d3daecfc4d
Added unit tests for function in ListUtils to randomly sample lists with replacement, updated AlleleFrequencyEstimate to provide a callType of HomRef, HetSNP, HomSNP, update indices in CoverageEval.py, and made a lot of changes to CoverageWalker biggest one being that it directly calls SingleSampleGenotyper instead of implementing some parts of SSG itself.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1189 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 02:05:40 +00:00
1db15ee468
made some things protected so that I can inherit them in MultiSampleCallerAccuracyTest
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1185 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-07 15:50:28 +00:00
1fa71aa31d
Now outputs stats. Doesn't do the downsampling thing because I think I'll have enough counts.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1184 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-07 15:29:31 +00:00
b9d533042e
Two-tailed HardyWeinberg test implemented. VariantEval now separate violations from summary outputs for clarity; Fixing problems with CovariateCounterTest and TabularRodTest
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1177 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-06 22:02:04 +00:00
depristo
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