31d2f04368
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-23 09:23:03 -05:00
966387ca0b
Next intermediate commit in the pool caller. Lots of bug fixes and now we can emit true vcf's with calls in discovery mode (still of unknown quality) - old validation mode is temporarily broken,will be fixed in next refactoring.
2012-01-23 09:22:31 -05:00
4a08e8ca6e
Minor tweaks to T2D-related qscripts. Replacing old md5s from the BeagleIntegrationTest. All differences boiled down either to the accounting of genotypes changed (./. --> 0/0 is no longer a "changed" genotype, and original genotypes that were ./. are represented as OG=. rather than OG=./. .)
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This is somewhat of an arbitrary decision, and is negotiable. I could see treating
GT:PL ./.:.
differently from
GT:PL .:0,3,6
but am not sure the worth of doing so.
2012-01-23 08:25:34 -05:00
4d6312d4ea
HaplotypeCaller is now an ActiveRegionWalker.
2012-01-22 14:31:01 -05:00
3b1aad4f17
After a minor and abject freakout, alter the T2D script to seek out truth sensitivities between 80 and 100, rather than between 0.8 and 1. Also, don't consider a genotype "changed by beagle" if the initial genotype is a no-call.
2012-01-20 23:43:51 -05:00
9b4f6afa21
Alterations to scripts for better performance. Grid search now expands the sens/spec tradeoff (90 was far too aggressive against hapmap chr20), and 20 max gaussians was too many, and caused errors. For consensus genotypes: remember to gunzip the beagle outputs before converting to VCF. Also, beagle can in fact create 'null' alleles in certain circumstances. I'm not sure what exactly those circumstances are, but those sites should be ignored. When it does, all alleles apear to be set to null, so this should not affect the actual phasing in the output VCF.
2012-01-20 23:07:59 -05:00
4b18786b5d
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-19 22:05:20 -05:00
ace9333068
Active region walkers can now see the reads in a buffer around thier active reigons. This buffer size is specified as a walker annotation. Intervals are internally extended by this buffer size so that the extra reads make their way through the traversal engine but the walker author only needs to see the original interval. Also, several corner case bug fixes in active region traversal.
2012-01-19 22:05:08 -05:00
066da80a3d
Added KEEP_UNCONDTIONAL option which permits even sites with only filtered records to be included as unfiltered sites in the output
2012-01-19 18:19:58 -05:00
7f3ad25b01
Adding a mode to VariantFiltration to invalidate previously-applied filters to allow complete re-filtering of a VCF.
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T2D VQSR: re-calling now done with appropriate quality settings and using BAQ.
2012-01-19 10:54:48 -05:00
7e082c7750
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-19 09:11:23 -05:00
ab8f499bc3
Annotate with FS even for filtered sites
2012-01-18 22:04:51 -05:00
b123416c4c
Resolve stale merge changes
2012-01-18 20:56:36 -05:00
2eb45340e1
Initial, raw, mostly untested version of new pool caller that also does allele discovery. Still needs debugging/refining. Main modification is that there is a new operation mode, set by argument -ALLELE_DISCOVERY_MODE, which if true will determine optimal alt allele at each computable site and will compute AC distribution on it. Current implementation is not working yet if there's more than one pool and it will only output biallelic sites, no functionality for true multi-allelics yet
2012-01-18 20:54:10 -05:00
0268da7560
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-18 09:53:00 -05:00
60024e0d7b
updating TDT integration test
2012-01-18 09:52:50 -05:00
11982b5a34
We no longer calculate the population-level TDT statistic if there are fewer than 5 trios with full genotype likelihood information. When there is a high degree of missingness the results are skewed or in the worst case come out as NaN.
2012-01-18 09:42:41 -05:00
763c81d520
No longer enforce MAX_ALLELE_SIZE in VCF codec
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-- Instead issue a warning when a large (>1MB) record is encountered
-- Optimized ref.getBytes()[i] => (byte)ref.charAt(i), which avoids an implicit O(n) allocation each iteration through computeReverseClipping()
2012-01-18 07:35:11 -05:00
0c7865fdb5
UnitTest for reverseAlleleClipping
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-- No code modified yet, just implementing a unit test to ensure correctness of the existing code
2012-01-18 07:35:11 -05:00
62801e430a
Bugfix for unnecessary optimization
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-- don't cache the ref bytes
2012-01-17 16:40:26 -05:00
f2b0575dee
Detect unreasonably large allele strings (>2^16) and throw an error
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-- samtools can emit alleles where the ref is 42M Ns and this caused the GATK (via tribble) to hang in several places.
-- Tribble was updated so we actually could read the line properly (rev. to 51 here).
-- Still the parsing algorithms in the GATK aren't happy with such a long allele. Instead of optimizing the code around an improper use case I put in a limit of 2^16 bp for any allele, and throw a meaningful exception when encountered.
2012-01-17 16:40:26 -05:00
8b0ddf0aaf
Adding notes to CountCovariates docs about using interval lists as database of known variation
2012-01-17 16:13:13 -05:00
40ebc17437
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-17 14:49:17 -05:00
41d70abe4e
At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.
2012-01-17 14:47:53 -05:00
ae259f81cc
Bug fixing for merging of read fragments when one fragment contained an indel
2012-01-17 14:39:27 -05:00
cde224746f
Bait Redesign supports baits that overlap, by picking only the start of intervals.
...
CalibrateGenotypeLikelihoods supports using an external VCF as input for genotype likelihoods. Currently can be a per-sample VCF, but has un-implemented methods for allowing a read-group VCF to be used.
Removed the old constrained genotyping code from UGE -- the trellis calculated is exactly the same as that done in the MLE AC estimate; so we should just re-use that one.
2012-01-17 13:51:05 -05:00
8e23c98dd9
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-17 13:46:28 -05:00
32ccde374b
Merged bug fix from Stable into Unstable
2012-01-17 11:08:35 -05:00
3ba918aff1
Error message cleanup in BAM indexing code.
2012-01-17 11:05:42 -05:00
cec7107762
Better location for the downsampling of reads in PrintReads
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* using the filter() instead of map() makes for a cleaner walker.
* renaming the unit tests to make more sense with the other unit and integration tests
2012-01-14 14:06:09 -05:00
b06074d6e7
Updated SortingVCFWriterBase to use PriorityBlockingQueue so that the class is thread-safe
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-- Uses PriorityBlockingQueue instead of PriorityQueue
-- synchronized keywords added to all key functions that modify internal state
Note that this hasn't been tested extensivesly. Based on report:
http://getsatisfaction.com/gsa/topics/missing_loci_output_in_multi_thread_mode_when_implement_sortingvcfwriterbase?utm_content=topic_link&utm_medium=email&utm_source=new_topic
2012-01-13 09:33:16 -05:00
28aa353501
Added "unbiased" downsampling parameter to PrintReads
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* also cleaned up and updated part of the unit tests for print reads. Needs a more thorough cleaning.
2012-01-12 16:33:55 -05:00
2c3176eb80
Merged bug fix from Stable into Unstable
2012-01-12 13:31:10 -05:00
cd43f016ce
Fixed NPE in getNextOverlappingBAMScheduleEntry() when mixed mapped/unmapped interval lists are used. Added integrationtest to verify behavior.
2012-01-12 13:29:11 -05:00
ed34b4f088
Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-12 10:27:26 -05:00
e7fe9910f7
Create the temp storage for calculating cell values just once as per Mark's TODO
2012-01-12 10:27:10 -05:00
f5f5ed5dcd
Don't initialize the cell conformation values (use an else in the loop instead) as per Mark's TODO
2012-01-12 08:50:03 -05:00
410a340ef5
Swapping the iteration order to run over AF conformations and then samples instead of the reverse minimizes calls to HashMap.get; instead of it being O(n) since we called it for each sample it's now O(1). Runtime on T2D GENES test set is reduced by 5-10%. More optimizations to follow.
2012-01-12 02:04:03 -05:00
77a03c9709
Patching special case in the adaptor clipping
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* if the adaptor boundary is more than MAXIMUM_ADAPTOR_SIZE bases away from the read, then let's not clip anything and consider the fragment to be undetermined for this read pair.
* updated md5's accordingly
2012-01-11 17:47:44 -05:00
25d0d53d88
Moving the approximate summing of log10 vals to MathUtils; keeping the more efficient implementation of fast rounding.
2012-01-10 12:38:47 -05:00
589397d611
Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-10 12:36:48 -05:00
c5320ef1af
Resolving changes in integration test during merge
2012-01-10 12:14:16 -05:00
e923a2e512
Revving Picard to incorporate final version of ReadWalker performance improvements.
2012-01-10 12:12:33 -05:00
0f36f6947e
Resolving merge conflicts
2012-01-10 11:44:16 -05:00
f2cecce10f
Much better implementation of the approximate summing of an array of log10 values (including more efficient rounding). Now effectively takes 0% of UG runtime on T2D GENES (as opposed to 11% previously).
2012-01-10 11:34:23 -05:00
509c3d87b0
Merged bug fix from Stable into Unstable
2012-01-09 23:08:46 -05:00
dc60757b68
Eliminate unnecessary strong references (and therefore memory held) by tree reduce entries that have already been processed.
...
Thanks to Tim Fennell for the bug report.
2012-01-09 23:04:53 -05:00
fda1795791
Merged bug fix from Stable into Unstable
2012-01-08 22:04:44 -05:00
1f1233b669
Fix for a rare but insidious bug in position tracking during async BAM file reading.
...
Thanks to Khalid for spotting and reporting the issue.
2012-01-08 22:03:35 -05:00
5793625592
No more "Q-<pid>@<host>". Generated log file names now use the first output + ".out" (ex. my.vcf.out) or the name of the first QScript plus the order the function was added (ex. MyScript-1.out). The same function added twice with the same outputs will now have the same default logs, meaning the 2nd instance of the function won't be added to the graph twice.
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QScript accessor to QSettings to specify a default runName and other default function settings.
Because log files are no longer pseudo-random their presense can be used to tell if a job without other file outputs is "done". For now still using the log's .done file in addition to original outputs.
Gathered log files concatenate all log files together into the stdout.
InProcessFunctions now have PrintStreams for stdout and stderr.
Updated ivy to use commons-io 2.1 for copying logs to the stdout PrintStream. Removed snakeyaml.
During graph tracking of outputs the Index files, and now BAM MD5s, are tracked with the gathering of the original file.
In Queue generated wrappers for the GATK the Index and MD5s used for tracking are switched to private scope.
Added more detailed output when running with -l DEBUG.
Simplified graphviz visualization for additional debugging.
Switched usage of the scala class 'List' to the trait 'Seq' (think java.util.ArrayList vs. using the interface java.util.List)
Minor cleanup to build including sending ant gsalib to R's default libloc.
2012-01-08 12:11:55 -05:00
Guillermo del Angel
Christopher Hartl
Ryan Poplin
Menachem Fromer
Eric Banks
Mark DePristo
Matt Hanna
Mauricio Carneiro
Khalid Shakir