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1455 Commits (7cf9a54b6485ea7319c3eddf098a3b7106c499ad)

Author SHA1 Message Date
depristo 7cf9a54b64 change for new char/byte in BaseUtils 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1467 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-27 23:47:56 +00:00
depristo a639459112 Trival consistency change from char in to char out, not char in to byte out 
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
chartl 6012f7602b @ minor fixes to CoverageAndPowerWalker and AnalyzePowerWalker (switching to By Reference traversal, spitting out Syzygy position for sanity check) 
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
chartl bd1e679bc5 @ Fixed issues with AnalyzePowerWalker which depended on CoverageAndPowerWalker. The latter was changed but not the former. Now fixed 
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
kiran 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.). 
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
chartl 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. 
@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
chartl 1da45cffb3 New: 
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
chartl 92ea947c33 Added binomProbabilityLog(int k, int n, double p) to MathUtils: 
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
kiran 478f426727 Fixed a missing method implementation in these two files. 
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
kiran 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. 
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
hanna 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. 
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
aaron 811503d67b vcf changes from Richards comments, fixed a test case 
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
andrewk ee05ddde16 Added command line options to make the barcode analysis script executable by end users. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1455 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-24 21:15:09 +00:00
hanna ccdb4a0313 General-purpose management of output streams. 
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
aaron b316abd20f catch a malformed column header name more gracefully 
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
aaron 0364f8e989 added the ability of the VCFReader to take in compressed gzipped files natively, which is really useful for the validator 
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
aaron 647a367680 Made the size zero interval file checker emit a warnUser if we're not in unsafe mode. 
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
aaron 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) 
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
aaron 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. 
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
asivache 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. 
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
aaron 6313c465fb we want the RMS of the reads qualities not the RMS of the RMS of the read qualities. 
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
kcibul 6c0adc9145 resuse fasta file reader 
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
aaron 0386e110cf some documentation changes, add a couple of simple checks 
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
aaron 026e09ec07 adding the package description for the VCF validator 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1444 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-20 04:46:27 +00:00
ebanks 10c98c418b Walker to determine the concordance of 2 genotype call sets. 
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
ebanks 1d74143ef4 A convenience argument - for Mark - so that you don't have to specify all the output file names 
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
aaron 5725de56dc fixes in VCF, some changes to get it ready to move out of the GATK 
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
aaron 0b927f44fa created a better seperation between instantiation of an VCF object and the object itself 
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
ebanks ed8c92a12a make isReference do the right thing 
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
hanna 21091b9839 Fix for invalid format error when outputting BAM files. 
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
aaron 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. 
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
ebanks b3fe566c0c Fix descriptions of walker args 
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
ebanks 82e2b7017e Prevent array bounds errors 
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
ebanks 26a6f816c9 set default value for output format 
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
ebanks 53153fcd79 Allow RODs to specify that incomplete records are okay (i.e. that they allow optional fields) 
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
ebanks 9b1d7921e8 added filter based on concordance to another call set 
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
ebanks b2a18a9d61 - first pass at a basic indel filter (for now, based on size and homopolymer runs) 
- 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
ebanks 78439f7305 Modify Sequenom input format based on official documentation 
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
aaron 63d90702d6 another iteration of the VCFReader and VCFRecord, introducing the VCFWriter 
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
jmaguire 1e8b97b560 quietly skip empty intervals files rather than crash. 
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
jmaguire 92c63fb530 It's just "lod" not discovery_lod now. 
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
ebanks df5744bcd3 update this walker so any variants can be passed in 
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
aaron 8403618846 the start to the VCF implementation 
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
ebanks d4808433a1 Added option to output the locations of indels in the alternate reference 
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
ebanks 4b6ddc55bd Merge our 2 fastq writers into 1: incorporate Kiran's secondary-base file writer into the fasta/fastq writers 
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
asivache 843d7e6c8f Now you can specify '-' instead of input file name, and the script will read from stdin 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1422 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-14 20:30:56 +00:00
ebanks 0ec581080c Refactoring the code; also, now it prints continuously instead of potentially storing one long string. 
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
asivache 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 
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
asivache 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). 
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
asivache 112a283f54 be nice, don't forget to close the reader when done 
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