76efa757f0
Switched over to reviewed version of Picard patch. In process, did some optimization to the IntervalSharder
...
which improved startup time 5-10x when dynamically merging many BAMs.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3331 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-08 14:12:22 +00:00
4617abf1ff
Fix bug in the interval sharder in cases where contigs specified in intervals are not present in any supplied BAM file.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3268 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-28 20:42:04 +00:00
c1e53d407d
The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had
...
unicode quote characters embedded in it. These characters were invisible inside
IntelliJ but cause compile warnings for Ryan and Aaron, who for whatever reason
have a different default charset. Fixed.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3203 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 15:26:32 +00:00
1bc26f69e9
An attempt to cleanup the Utils directory. Email to follow.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3198 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-19 23:00:08 +00:00
400684542c
Revisions to take into account finalization of Picard patch: naming changes, better definition
...
of public interfaces. This won't be the last Picard patch, but it should be the last big one.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3096 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-30 19:28:14 +00:00
85037ab13f
Fix for Kiran's sharding issue (Invalid GZIP header). General cleanup of
...
Picard patch, including move of some of the Picard private classes we use to Picard public.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3087 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-29 03:21:27 +00:00
46c14ec63f
New, much less memory intensive implementation of BAM file sharding. Streams indices together with the expectation
...
that bins will be present in the bin sparse array, which avoids the problem of having to hold the sparse bin array
stored in every BAM file index in memory at the same time.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3075 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-25 17:41:22 +00:00
884a577013
Phase 2 of Picard patch refactoring: kill off SAMFileReader2/BAMFileReader2, merging the changes back into the base classes.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3065 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-23 16:48:11 +00:00
b4b4e8d672
For Sarah Calvo: initial implementation of read pair traversal, for BAM files
...
sorted by read name.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3052 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-21 23:22:25 +00:00
c0eb5c27ea
Lower memory support for merged sharding. Merged sharding is still not available.
...
WARNING: If you update frequently, you might have to rm -rf ~/.ant/cache -- this is an unfortunate side effect of the way we
distribute picard-private.jar.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3050 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-19 22:03:47 +00:00
45f70de6df
Fixed bug that failed to reset an accumulator when crossing contig boundaries,
...
meaning that in special cases of shallow coverage, an interval might get dropped.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2999 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-15 04:45:55 +00:00
88a48821ea
removed the dependence on removeRegion() in GenomeLocSortedSet
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2993 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-12 22:35:49 +00:00
7aa7a5f9b8
Bug fixes for edge cases and filtration in the earlier performance fixes.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2989 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-12 04:46:08 +00:00
5e8654fcdc
Oops! Introduced a performance bug in read interval sharding, when the new sharding system is available. Track more state to avoid this problem in the future.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2987 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-11 23:19:42 +00:00
cbd529d544
Better chopping up of data for ref walkers.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2982 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-11 20:13:26 +00:00
e4360bac6a
More comprehensive support when sharding for ref walkers.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2951 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-08 11:25:20 +00:00
a7fe07c404
A few stopgap fixes to get the GATK to the point where the old sharding
...
infrastructure can be torn down:
1) New sharding system emulates old MonolithicSharding mechanism.
2) Better awareness of differences between fasta and BAM files when creating
shards.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2948 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-07 21:01:25 +00:00
1ef1091f7c
Cleanup and simplification of read interval sharding.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2944 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-05 23:34:38 +00:00
adea38fd5e
Sharding system fixes for corner cases generally related to lack of coverage
...
in the BAM file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2928 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-04 18:59:21 +00:00
6133d73bf0
Locus (non-intervalled) traversal with new sharding system.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2903 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-01 01:58:44 +00:00
80f5d2829d
Support for read interval sharding with proper filtering.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2902 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-27 20:26:34 +00:00
b69c2d0f70
Cleanup. Remove some unnecessary methods.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2900 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-26 21:50:48 +00:00
30eb28886b
Basic functionality for intervaled reads in new sharding system. Not currently filtering out cruft, so
...
the mode of operation is currently queryOverlapping rather than queryContained.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2899 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-26 21:41:55 +00:00
1017a38f38
Initial refactoring of read traversal to make it easier to drop in intervalled reads traversal.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2894 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-26 15:09:09 +00:00
553d39bb00
Clean up the code a bit following the introduction of reduceByInterval.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2887 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-25 01:20:22 +00:00
fff15944fe
Bug fix. Stopping condition of recurrence stopped too soon in some cases where an interval *contained* zero reads but *overlapped* with some reads.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2874 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-23 15:58:54 +00:00
a0e8de40cf
Bug fix: at one locus in the dataset, two reads were dropped.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2872 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-22 23:54:52 +00:00
88d0677379
Misc correctness enhancements: develop the bin selector into a recursive algorithm and return a shard when reads are missing. Also improve the performance of the read filter that clips reads not actually present in the shard.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2870 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-22 22:19:06 +00:00
cc09f48cd8
Correctness fix: index can concat chunks around shard edges, and my code didn't account for that.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2861 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-19 21:44:33 +00:00
71f18e941f
Significant performance improvements made by subtracting out the contents of the prior highest-level bin.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2859 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-19 16:46:16 +00:00
232d884578
Got back most of the performance lost when I fixed the dropped reads problem.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2835 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-12 19:59:56 +00:00
77af5822d4
Correcting my incomplete understanding of how the BAM file index actually works.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2833 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-12 16:15:19 +00:00
0250338ce7
Basic use cases for merging BAM files with the new sharding system work.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2815 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-09 22:14:37 +00:00
e53432d54d
Checkpoint for combining adjacent intervals into the same shard.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2782 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-05 02:48:02 +00:00
e7f5c93fe5
Cleaning up the inheritance hierarchy from the previous commit.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2738 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-29 19:13:36 +00:00
3d922a019f
Basic support for very simple index-driven locus traversals. Interface has been changed to
...
support batched intervals in a single shard, but intervals are not yet compressed into a single
shard.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2730 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-29 03:14:26 +00:00
b19bb19f3d
First successful test of new sharding system prototype. Can traverse over reads from a single
...
BAM file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2587 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 03:35:55 +00:00
16777e3875
more fixes for the empty interval list problem; you can now run LocusWindow traversals with an empty interval list, but the GATK will give you a warning (unless you're running in unsafe mode).
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2563 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-12 18:47:43 +00:00
3c5f5177b1
check to see if the parsed interval list is empty, since we now allow interval files that are empty. If so, make sure we default to a non-interval based traversal.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2559 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-12 17:52:27 +00:00
e6127cd6c5
Temporary hack for Tim Fennell: introduce a sharding strategy that stuffs all data into a single
...
shard for cases when the index file isn't available. Works for the case in question, but is not
guaranteed to work in general. Will be replaced once the new sharding system comes online.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2383 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-16 21:55:42 +00:00
4c147329a9
Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file
...
in GenomeAnalysisTK.jar. Still no support for actually displaying the archived javadoc. Also change the approach
to providing package javadocs: retired the deprecated package.html file in favor of Java1.5-style package-info.java.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2263 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 20:08:41 +00:00
fc1c76f1d2
fixing a bug where reads in overlapping interval based locus traversals could get assigned to only one of two the regions
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1407 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-11 17:50:16 +00:00
bcb64d92e9
Aaron: 1, GenomeLoc: 0. I changed our GenomeLoc class, seperating the creation of a genome loc (with the reference setup) to a parser class. GenomeLoc now just represents the actual genomic postion. The constructors are now package-protected (to enforce using the parser), but we may want to expose some constructors in the future.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1069 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-22 14:39:41 +00:00
43a28750e0
Package level documentation -- helps new users get acclimated to the codebase more quickly.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1029 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 16:27:48 +00:00
63b5c12cbd
Changed dataSources to datasources, to be consistant with the rest of our package names. Also, this makes me champion in the largest check-in contest.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@985 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-11 18:13:22 +00:00
hanna
aaron