b4df089b59Putting some of the required data structures together for imperfect lookup.
hanna
2009-09-17 22:43:11 +0000
355136928ePlay nice with other jobs in this VM -- don't close stdout / stderr.
hanna
2009-09-17 18:55:08 +0000
0e73b2ba8eUse population allele frequencies to distinguish between top candidates
sjia
2009-09-17 15:49:19 +0000
534486a254Output formatting changed: - summary output now reported as a percentage rather than proportion; 2 sigfigs - fixed minor bug where FNR was calculated over total calls rather than total variant sites - column headers are_now_contiguous_strings - spacing fixed - "No Call" separated from "Ref Call" as its own column
chartl
2009-09-17 14:00:25 +0000
73bec6f36dNow uses expanding array list for coverage histograms. No hard limit on maximum depth now
depristo
2009-09-16 23:27:25 +0000
4ad46590a3Changes to PooledGenotypeConcordance:
chartl
2009-09-16 21:45:01 +0000
3e289fcaa4A little piece that PairMaker needs in order to compile ;) Iterates synchronously over two (name-ordered) single-end alignment SAM files with, possibly, multiple alignments per read and for each read name encountered returns pairs<all alignments for end1, all alignments for end2>
asivache
2009-09-16 19:17:40 +0000
598974ae10perl script to make batching jobs easier
ebanks
2009-09-16 19:02:46 +0000
2f29cf59baVery early, half-baked version. All it can do right now is to take two SAM files with end1 and end2 individual single-end alignmnets from a pair-end run and spit out a "paired" BAM file that contains ONLY properly paired ends (both ends align uniquely && both ends align to the same chromosome && the ends align in proper orientation). Insert size is currently not used (and not set in the output). Unpaired/unmapped reads are NOT transferred into the output bam. For the pairs that do get written, the output is (should be) standard-conforming: all flags are properly set and mate pair information is correct.
asivache
2009-09-16 18:38:18 +0000
5d85bd9671By default, VF should ask for deleted bases so that they show up in coverage. The Strand filter then needs to ignore those bases when determining bias.
ebanks
2009-09-16 16:46:09 +0000
a7c306f757-deal with offsets that can be -1 -added option to have "D"s inserted for deleted bases in pileup strings
ebanks
2009-09-16 16:44:57 +0000
01a9b1c63bFix for problem where err stream remapped to output stream in certain cases, (hopefully) completing Matt's hat trick of fail. Thanks, unit tests.
hanna
2009-09-16 08:33:56 +0000
eedf55e94dtemp fix for a broken test, we'll fix the test tomorrow. We promise, we're engineers, we love our tests.
aaron
2009-09-16 04:36:42 +0000
9f7cf73411Output stream management fixes. I completely screwed up the output stream management system, but cleverly masked this fact by breaking some other stream management functionality that masked the problem.
hanna
2009-09-15 21:06:45 +0000
17758b381cProperly initialize redirected output streams in case of out and err.
hanna
2009-09-15 19:47:43 +0000
00dfe014b7Added option to FastaReferenceWalker to change output FASTA file format's line width and to remove header lines; allows dumping raw sequence using intervals
andrewk
2009-09-15 18:00:30 +0000
b69eb208a6Always create output files, even if no output was written to them.
hanna
2009-09-15 17:58:14 +0000
8f9dd03e87Get rid of unnecessary files for generating recalibration data.
hanna
2009-09-15 15:53:06 +0000
e6827424b9Added support python and R scripts for generating covariate output graphs.
hanna
2009-09-15 14:17:36 +0000
b401929e41incremental clean-up and changes for VariantEval, moved DiploidGenotype to a better home, and fixed a spelling error.
aaron
2009-09-15 04:48:42 +0000
6783fda42aUpdated unit test to reflect changes to vcf output
ebanks
2009-09-15 01:56:08 +0000
fb254759cbTrivial: Don't print reduce result
andrewk
2009-09-14 23:42:20 +0000
d191e02c88Automated parsing stats from VariantEval and outputting stats to "*.oneline_stats" files; needed to do larger culling of predictions vs. actual SNP call for Pilot 3 lanes
andrewk
2009-09-14 23:40:11 +0000
e06e31d99fMany generalization improvements - parameters, files as options - to script that runs pieces for predicting SNP calling performance for given SNP calling coverage
andrewk
2009-09-14 23:37:53 +0000
7eb21e55c1Added die_on_fail which outputs an error message and stops execution if a farm or terminal command fails
andrewk
2009-09-14 23:30:13 +0000
118071cfd8Proof-of-concept perfect read aligner, implemented as described in sec 2.4 of BWA paper. Has successfully aligned a handful of reads. Requires significant cleanup and refactoring.
hanna
2009-09-14 21:54:56 +0000
01e7b39c8d1. Don't print out values in filter field of the VCF. 2. Fix ratio printouts (for params file) 3. Rename ratio filter's get counts method to avoid confusion; more changes on the way this week.
ebanks
2009-09-14 21:03:39 +0000
436f543b3bI owe Doug a beer for finding this: don't print out intervals to be merged if they're not within the global -L intervals
ebanks
2009-09-14 20:22:30 +0000
9be1832d7bPhasing version 1
sjia
2009-09-14 16:10:37 +0000
a009592662the life in the magical kingdom of fully spec-conforming SAM files would be so... magical. For now, however, there are plenty of ways to end up with inconsistent SAM records. For instance, a SAM file with missing header will result in SAM records with ref. name set, but getReferenceIndex() returning null. This, in turn, was tripping isReadUnmapped(). The method is now fixed, so that it suffices to have *either* reference name *or* reference index set for the read to be considered mapped (the flag is still checked)
asivache
2009-09-14 16:04:19 +0000
e03fccb223Changes to switch Variant Eval over to the new Variation system.
aaron
2009-09-14 05:34:33 +0000
0feee9cdfdfinished up modularized pipeline; needs some testing but is generally done.
ebanks
2009-09-14 02:41:57 +0000
5b41ef5f70rod DBSNP had a bug where the reference wasn't calculated correctly under certain conditions. Fixed getRefBasesFWD and getRefSnpFWD so that they were more in line with getAltBasesFWD and getAltSnpFWD. Also updated Variant Eval tests to reflect this change.
aaron
2009-09-13 23:48:58 +0000
5cf1d6c104Bugfix - this walker was never changed to work with the new PoolUtils methods after those methods were changed to return ReadOffsetQuad objects rather than nested pairs. This broke the build :(.
chartl
2009-09-13 19:39:23 +0000
c669e8d5adUse constant seed in the random generator so we can be stable (and thus unit tests will work)
ebanks
2009-09-13 17:40:56 +0000
15178977e1Naive tool to convert from vcf to geli text
ebanks
2009-09-13 17:25:02 +0000
84c8374e682nd stab at creating a pipeline [not quite finished yet]. Modularized the system to emulate what it will look like in firehose.
ebanks
2009-09-13 05:53:18 +0000
794bd26b20Changed some ShortNames so they made more sense.
chartl
2009-09-13 01:32:12 +0000
b353bd6f81Added a Quad toString() method.
chartl
2009-09-13 01:13:57 +0000
2e237a12e9This commit has a bunch to do with cleaning up the CoverageAndPowerWalker code: implementing some new printing options, but mostly altering the code so it's much more readable and understandable, and much less hacky-looking.
chartl
2009-09-13 01:00:04 +0000
275707f5f6Data structure for counts, to isolate the user from wonky 'sometimes counts are cumulative, other times base-by-base' gotchas.
hanna
2009-09-11 20:53:24 +0000
7c8b17b456fix for SSG with pl name
depristo
2009-09-11 20:39:34 +0000
5354c1876cDe Novo SNP caller as presented at 1KG meeting on 9/10/09 with min LOD 5 calls required from both parents and a LOD 5 call in the daugter gold standard concordant call set. All SNP calls must be present as bound RODs.
andrewk
2009-09-11 19:30:23 +0000
0f3049652aStart to build BWT abstractions, so we can present a reasonable facsimile of the BWT to the user no matter how it's represented on disk.
hanna
2009-09-11 18:23:15 +0000
c3f77acd5eAlteration to CoverageAndPowerWalker. It can now be flagged with -uc which will cause it to print not only the coverage on each strand that exceeds the quality score threshold, but also the total coverage on each strand as well.
chartl
2009-09-11 17:55:44 +0000
702ba553d6Some useful scripts for running only individual parts of the pilot1/2 cleaning/calling pipeline
ebanks
2009-09-11 17:38:33 +0000
f3f5e849cbSSG now in early access
depristo
2009-09-10 16:45:19 +0000
e24c8d00d5So, the VCF spec allows for an optional meta field in the header representing the date. However, using this field means that integration tests run on the vcf file will fail the MD5 test (which is what happened to the VariantFiltration test this morning after working just fine yesterday). After consulting our resident expert (Aaron), we're going to (temporarily) remove the date from the vcf output until we can come up with a better solution. However, this shouldn't cause any short-term problems because the data truly is optional. VF test's MD5s are updated.
ebanks
2009-09-10 14:28:43 +0000
fc0d9578f6better feedback now
depristo
2009-09-10 12:43:45 +0000
296878e8e3adding a basic implementation of the Variation interface.
aaron
2009-09-10 04:41:13 +0000
5a64a80ab5changes to the variation class, updates to SSG, updated tests based on changes to the SSGenotypeCall, and added the ability to run a single integration test from using the build script.
aaron
2009-09-10 04:31:33 +0000
c988205884Notes for Aaron in SSG
depristo
2009-09-10 03:18:51 +0000
1362a56227Added fasta tests and small fix to cleaner test
ebanks
2009-09-10 03:13:11 +0000
8ca89279aaAdded a test for VariantFiltration and the VECs
ebanks
2009-09-10 02:21:14 +0000
6de54dcd2aHigher-level readers and writers for BWTs and suffix arrays.
hanna
2009-09-09 22:45:32 +0000
0093482c62N reference base fix for SSG
depristo
2009-09-09 21:19:36 +0000
bc9fe31cf5Cleanup of int-packed file readers / writers. All primitive writers for BWTs and SAs are in place; time to move on to compound reader / writers.
hanna
2009-09-09 20:36:39 +0000
d9f3e9493fDoes not return 0-length cigar elements anymore (used to do so when previous cigar element ended exactly at the segment boundary)
asivache
2009-09-09 20:05:55 +0000
cb31d5a0abVariantFiltration now outputs VCF. Important changes: 1. VariantsToVCF can now be called statically to output VCF for a single ROD instance; this is temporary until we have a VCF ROD. 2. VariantFiltration now outputs only 2 files, both mandatory: all variants that pass filters in geli text, and all variants in VCF. If there are any problems, go find Aaron.
ebanks
2009-09-09 20:04:32 +0000
dd0085c4281) now is tolerant to sloppy cigar strings with 0-length elements (at the price of extra recursive call) 2) when reads with deletions are requested, adds to the pile just those: reads with 'D' over the current reference base, but not 'N' 3) next() now implements a loop: recursive forward iteration calls to next() until ref. position with non-zero coverage is encountered were OK for (short) deletions, but with long stretches of N's they end up with stack overflow
asivache
2009-09-09 20:04:04 +0000
542af6402eoutput correct format for Sequenom SNPs
ebanks
2009-09-09 19:21:53 +0000
43d1c6741cCleanup. Separate common packing functionality into utils class. Make base packing utility as generic as possible.
hanna
2009-09-09 17:54:12 +0000
3b1e966b4cLowercases the sequencing platform so that a difference in case doesn't lead to the failure to look up an entry in the hash.
kiran
2009-09-09 17:35:45 +0000
d82d6c0665Excludes variants that fall below a certain LOD that changes as a function of depth.
kiran
2009-09-09 17:34:16 +0000
06eae52292Throws an exception if you attempt to use a filter that doesn't exist.
kiran
2009-09-09 17:33:27 +0000
1060b36288Bug fix: 'N' cigar elements now treated properly; for all practical intents and purposes, N is the same as D and should be treated as such, the difference is only in logical interpretation.
asivache
2009-09-09 17:08:35 +0000
bed646e4f6Adding cleaner test
ebanks
2009-09-09 16:05:56 +0000
9c7f456510Changed the short name on the PoolSize cmd line argument
chartl
2009-09-09 15:53:22 +0000
d9588e6083bug fixes to LIBS and LIBH following ultra-aggressive regression testing across 454, solid, and solexa
depristo
2009-09-09 15:36:12 +0000
0721c450c2Bug fix: single unmapped read now keeps mapping qual 0 after remapping, not 37!
asivache
2009-09-09 15:29:34 +0000
df11618092Set default value of useLocusIteratorByHanger to FALSE. Otherwise the -LIBH flag is useless and there'd be no wayto "unset" the 'true' value. Old version was (always) using LocusIteratorByHanger. Now default iterator is indeed LocusIteratorByState, and -LIBH will switch back to the old one
asivache
2009-09-09 15:09:09 +0000
0df6a9da5c-Seperating out normal (unit) tests and integration tests. From now on if your test are more of an integration test (i.e. you're testing a walker and all the subunits it relies on) please name the test "______IntegrationTest.java" instead of "______Test.java".
aaron
2009-09-09 15:01:40 +0000
eeb9b6eb13GenotypeLikelhoods now support a cache per subclass, avoiding genotyping clashes
depristo
2009-09-09 10:39:14 +0000
0cc219c0df-Added unit test for walkers dealing with intervals for cleaning -I also uncovered a corner case in the cleaner that for some reason was commented out but shouldn't have been. Hooray for unit tests!
ebanks
2009-09-09 02:35:17 +0000
ec0f6f23c7LocusIterationByState is now the system deafult. Fixed Aaron's build problem
depristo
2009-09-09 01:28:05 +0000
ea6ffd3796initial VariantEvalWalker test. More to be added soon...
aaron
2009-09-09 01:02:04 +0000
adce3bd536My reference implementation is now generating a BWT which matches BWT-SW's. Note to self: never give project status in an svn log.
hanna
2009-09-08 22:11:03 +0000
f22f590192Successfully writing .sa files.
hanna
2009-09-08 17:34:34 +0000
600c234643Starting code on phasing
sjia
2009-09-08 15:20:38 +0000
hanna
sjia
chartl
depristo
asivache
ebanks
aaron
andrewk
kiran