bdd0a6f9fa
change to make build work
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1511 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-03 13:43:10 +00:00
b01ac9de0c
High performance LocusIterator implementation. Now with greatly reduced memory impact and 2x (and more potentially) speed ups of raw locus iteration. General performance improvements to SSG with empirical probs. You can enable high-performance locus iteration with the -LIBS arg. It's still testing but passes validing pileup.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1510 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-03 03:06:25 +00:00
e2780c17af
Checkin of the Multi-Sample SNP caller.
...
Doesn't work yet; same command I used to use now causes GATK to throw an exception.
Will check with Matt & Aaron tomorrow, then do a regression test.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1509 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-03 00:23:28 +00:00
e2a79c5cd9
Checkpoint. The BWT that we generate now matches the first 16% of the BWT that BWT-SW generates. Cleaned up output streams to separate the byte packing / word packing from the data structure generation.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1508 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-02 22:18:17 +00:00
3dfc77dc89
Add an indel rod which represents the initial point of the indel only
...
(useful for alternate reference making)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1507 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-02 19:32:29 +00:00
58debd7e56
A convenience shortcut isReadUnmapped() added: thanks to SAM format specification, 'read unmapped' flag is not always required to be set for an unmapped read; this method checks both the flag and the alignment reference index/start (if those are set to '*' the flag is not required according to the spec!)
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1506 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-02 17:00:39 +00:00
0e6feff8f2
fixed locus pile-up limiting problem
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1505 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-02 16:56:44 +00:00
d8aff9a925
Bug fixes. Was ignoring the '$' character in a few places where I shouldn't have been.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1504 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-02 16:27:31 +00:00
55013eff78
Re-revert back to point estimation for now. We need to do this right, just not yet.
...
Also, it's safer to let colt do the log factorial calculations for us.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1503 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-02 15:33:18 +00:00
1ada085970
Cruddy implementation of BWT creation, for understanding and testing purposes.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1501 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-02 02:16:56 +00:00
24d809133d
Oops - comment out the printouts
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1500 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-02 01:45:56 +00:00
91ccb0f8c5
Revert to having these filters use integration over binomial probs
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1499 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-02 01:40:22 +00:00
05c164ec69
changing the default behavior to allow any sized read pile-up (which may exceed the memory limit); the user can then select their own read limit. The default of 100K was arbitrary.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1498 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-01 14:46:00 +00:00
54c0b6c430
Allow this ROD to consist of just the positions
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1497 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-01 12:43:18 +00:00
4a1d79cd7b
added a flag, maximum_reads_at_locus, shortName "mrl", which limits the number of reads we add to the locusByHanger. In some bam files misalignment produces pile-ups of 750K or more reads. We now limit this to the default of 100K reads.
...
The user is warned if a locus exceeds this threshold, and no more reads are added.
Also CombineDup walker had an incorrect package name.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1496 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-01 04:21:58 +00:00
0addae967a
IndelArtifact filter can now handle filtering false SNPs that occur within the span of an indel but after the first position
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1495 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-01 03:34:39 +00:00
85ca68fab6
Initial version: creates a packed file from a fasta, suitable for consumption by BWT-SW. Works with E coli fasta, but will not work at this moment with multi-chr fastas.
...
Will be made into a utility routine when BWA comes together.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1494 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-31 18:39:19 +00:00
591f8eedbb
Added setName() and getName() (however, not used anywhere yet). Now can set the name of the fasta record manually to whatever, however it will work only if done early enough. If the fasta record already started printing itself (i.e. the header line is already done), setName() will throw an exception. Could be too entangled, may reverse this back...
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1493 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-31 18:09:55 +00:00
c9eb193c7f
Now recognizes a special name for a bound rod track: snpmask. If a rod with this name is bound, then ONLY snps from that track will be used (to set alt reference bases to N's), but indels will be ignored. This helps when an alt. ref has to be created for a set of indel calls, and another rod (e.g. dbSNP) is used to put N's in (for sequenom). If dbSNP rod is not marked as "snpmask", the indels reported there will make their way into the alt. reference output and mess it up.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1492 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-31 18:05:57 +00:00
8e3c3324fa
Added filter for SNPs cleaned out by the realigner.
...
It uses the realigner output for filtering; in addition, dbsnp indels partially work; IndelGenotyper calls don't yet work.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1489 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-31 04:32:32 +00:00
8bc7afe781
Smarter SW penalties
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1488 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-31 04:29:19 +00:00
463f80c03e
Require each filter or feature to declare whether or not they want mapping quality zero reads in the alignment context
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1487 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-31 03:37:24 +00:00
1a299dd459
Require each filter or feature to declare whether or not they want mapping quality zero reads in the alignment context
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1486 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-31 03:31:37 +00:00
e70101febc
Add a VEC filter for clustered SNP calls that takes advantage of the new windowed approach; delete the old standalone walker.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1485 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-31 03:14:42 +00:00
215e908a11
Reworking of the VariantFiltration system to allow for a windowed view of variants and inclusion of more data to the various filters.
...
This now allows us to incorporate both the clustered SNP filter and a SNP-near-indels filter, which otherwise wasn't possible.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1484 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-31 02:16:39 +00:00
813a4e838f
Removing old code
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1482 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-30 19:27:11 +00:00
49a7babb2c
Better organization of Genotype likelihood calculations. NewHotness is now just GenotypeLikelihoods. There are 1, 3, and empirical base error models available as subclasses, along with a simple way to make this (see the factory).
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1481 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-30 19:16:30 +00:00
522e4a77ae
Caching support across multiple technologies
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1480 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-30 18:10:14 +00:00
5af4bb628b
Intermediate checking before code reorganization. Full blown support for empirical transition probs in SSG for all platforms. Support for defaultPlatform arg in SSG. Renaming classes for final cleanup
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1479 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-30 17:34:43 +00:00
6ab9ddf9f5
Significant output formatting improvements. SNPs as indels analysis. heterozygosity rate calculations
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1478 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-29 21:49:09 +00:00
bde67428fd
Better formatting of the code
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1477 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-29 21:46:47 +00:00
8331c195fb
changed the full name of maximum_reads to maximum_iterations for consistancy
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1475 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-28 16:03:46 +00:00
8e129d76fd
Support for original quality scores OQ flag. pQ flag in TableRecalibation to preserve quality scores below a threshold (defaulting to 5)
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1474 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-28 14:14:21 +00:00
f0179109fa
Removing min confidence for on/off genotype
...
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
4f7ed69242
toString() implemented
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1472 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-28 01:03:58 +00:00
dc9d40eb9a
Now requires a minimum genotype LOD before applying tests
...
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
37a9b84276
corresponding test
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1470 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-28 00:17:42 +00:00
bf60980653
Experitmental support for empirical P(B_true | B_miscall). --useEmpiricalTransitions flag to SSG enables this support. Much better implementation of Genotype likelihoods -- the system should scream along now. Continuing progress towards deleting old model
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1469 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-28 00:17:24 +00:00
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
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
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
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
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
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
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
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
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
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
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
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
depristo
jmaguire
hanna
ebanks
asivache
aaron
chartl
kiran