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
e5115409fa
Force columnSpacing to be at least one. We need a general-purpose, working tool for outputting columnar data to a PrintStream; will add JIRA.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1457 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-25 19:54:54 +00:00
811503d67b
vcf changes from Richards comments, fixed a test case
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1456 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-25 14:32:16 +00:00
ccdb4a0313
General-purpose management of output streams.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1454 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-23 00:56:02 +00:00
b316abd20f
catch a malformed column header name more gracefully
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1453 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-21 21:05:28 +00:00
0364f8e989
added the ability of the VCFReader to take in compressed gzipped files natively, which is really useful for the validator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1452 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-21 18:40:38 +00:00
647a367680
Made the size zero interval file checker emit a warnUser if we're not in unsafe mode.
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Also changed the default logger level from error to warn. Does anyone object? It makes sense for users to always get their warn user statements in the default logging level.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1451 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-21 14:40:57 +00:00
df9133c90b
the doc on File.length states it returns 0L if it doesn't exist, added a check to make sure it exists (and length < 1)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1450 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-21 05:55:17 +00:00
cd711d7697
Added detection of interval files with zero length to the GATK, and removed it from the interval merger walker: this was a critical blocking emergency issue for Eric.
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also fixed some verbage in the GAEngine.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1449 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-21 05:35:49 +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
6313c465fb
we want the RMS of the reads qualities not the RMS of the RMS of the read qualities.
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Also the VCF version tag seems to be standardized as VCR. Updated the VCF code.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1447 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-20 21:56:29 +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
0386e110cf
some documentation changes, add a couple of simple checks
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1445 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-20 05:20:27 +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
5725de56dc
fixes in VCF, some changes to get it ready to move out of the GATK
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1441 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-19 23:31:03 +00:00
0b927f44fa
created a better seperation between instantiation of an VCF object and the object itself
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1440 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-19 20:32:50 +00:00
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
chartl
kiran
hanna
aaron
asivache
kcibul
ebanks
jmaguire