8f1cabd33d
cmd line args changed - again; internally uses VariantType enum
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@818 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 21:03:58 +00:00
9ef1a21112
minor changes
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@817 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 21:03:06 +00:00
d994544c47
Added back end code support for Sharding based on genomic location for reads. Changed the sharding
...
code to take GenomeLocSortedSet instead of a list<GenomeLoc>, and added a bunch of much simplier
and cleaner test cases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@816 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 20:57:46 +00:00
4edcdffe45
refseq annotation track: should be able to provide (multiple) transcript annotations available over a given genomic position. NOT finished and NOT tested!
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@815 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 20:07:15 +00:00
149cc9989b
spaces!!!!!!!!!
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@814 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 19:40:25 +00:00
c2df35b7fe
- get leftmost position of indel correct
...
- don't try to clean reads with mapping quality of 0
- un-deprecate
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@813 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 17:24:58 +00:00
54bb643d19
Validated Mark's assertion that GSA-27 is fixed. Also did some cleanup on the pileup walker so that it doesn't output to System.out.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@812 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 15:58:21 +00:00
008d677bea
Fixed ValidatingPileup to work with Andrey's new rodSAMPileup -> GenotypeList type hierarchy.
...
Fixed reference-ordered data validation system to validate class hierarchies instead of specific class types.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@811 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-23 20:50:28 +00:00
d056f9f3e8
Changed the name to reflect the sorted nature of the set, added some fixes
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@810 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 22:34:24 +00:00
831d430025
Added a collection for storing GenomeLocs, that also has functions for removing by genomic region (that may span multiple GenomeLoc's in the collection), and adding regions, which are then merged with any overlapping regions.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@809 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 21:52:40 +00:00
34413362fd
Bugfix: handle case where queue is empty.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@808 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 21:45:22 +00:00
ec2e8d5726
Fixes for getting ValidatingPileup running in parallel.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@807 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 21:20:24 +00:00
cd80e3f372
Replaced dumb training function with a version that creates a training set slightly more sensibly.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@806 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 19:34:33 +00:00
02c0afdb85
Added the ability to specify the sorted, unaligned bam and/or the sorted, aligned bam such that broken computations can be restarted.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@805 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 19:33:34 +00:00
454a6d1df7
Fixed an egregious error in simpleReverseComplement wherein the RC'd string would be composed entirely of the last base.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@804 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 19:32:20 +00:00
2a5be1debe
Cleanup in datasources.providers namespace. Make it easier for others writing traversal engines to use.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@803 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 19:12:00 +00:00
02fc4f145f
refactoring: a couple of general purpose (hopefully useful?) methods/classes extracted into a standalone utils class
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@802 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 18:54:40 +00:00
4b718688d5
no changes, really, just synchronizing (instead of reversing) to increase the amount of entropy
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@801 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:27:28 +00:00
893f1b6427
updated
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@800 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:25:50 +00:00
a9dfbfb309
internal changes and some refactoring. slightly different final report. Now can take tracks that implement either Genotype or GenotypeList; takes an arg specifying what variants to look for (POINT - aka snp - or INDEL); takes an arg specifying whether default ref/ref call of one type (INDEL/POINT) should be implicitly assumed if another call (POINT/INDEL respectively) was made at the same position [this is probably most useful for indels and only (?) for sam pileups: if we have only point mutation call at a given position, it does mean that we do have coverage, and that there was no evidence whatsoever for an indel, so we have an implicit 'no-indel' call]
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@799 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:25:09 +00:00
d5bb4d9ba9
Auxiliary class that can read one line from samtools pileup file. Used by rodSAMPileup to read pairs of lines as needed. NOTE: this class implements Genotype and (a trivial) GenotypeList, but it is NOT a rod!
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@798 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:20:01 +00:00
732fed9aad
ALERT, ALERT! rodSAMPileup is now a GenotypeList, not a Genotype! Now it can intelligently read full samtools pileup files (containing, in general, both point and indel genotypes at the same position). No need to split/synchronize pileups from different individuals anymore, hooray!
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@797 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:17:59 +00:00
26633957d9
Genotype interface is extended: now it requires implementing object to be able to tell whether it isPointGenotype() or isIndelGenotype() (and the contract requires, e.g. alleles to be represented differently)
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@796 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:14:46 +00:00
d9fc84f1e3
actually checking in the first pass
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@795 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:13:27 +00:00
8773b3a430
a trivial wrapper interface for the objects capable of holding 'full' genotype, i.e. both point (as in ref/snp) and indel variants at the same reference position
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@794 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:12:01 +00:00
7a979859a9
Intermediate checking for evaluation -- now supports transition / transversion evaluation
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@793 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:05:06 +00:00
f2ea193149
For some reason the apostraphes in the comments were throwing annoying
...
compile-time warnings: "unmappable character for encoding UTF8"
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@792 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 14:07:07 +00:00
9902ce8073
properly flush the gzip output stream. this was a subtle inheritance bug.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@791 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 13:57:58 +00:00
63caca31bf
minor update in report printout format
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@790 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 13:56:09 +00:00
7afc10fd6f
updated, reports more stuff now, including stats for external consistency checks
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@789 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 22:28:18 +00:00
30c63daf89
More improvements to the duplicate quality combiner, making progress towards a clean system
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@788 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 22:26:57 +00:00
65995887fc
Releasable version of the Pileup walker
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@786 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 22:25:37 +00:00
dc17a5661d
Better accessors for dealing with second base prob pileups
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@785 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 22:25:16 +00:00
d261459c48
Useful function to create a string with N copies of a same char
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@784 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 22:23:52 +00:00
287bb52e81
Refreshes the mount points that we'll be using (so that the program will play nicely with LSF).
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@783 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 20:36:12 +00:00
b5ad5176f7
stick headers on the output tables
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@782 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 20:35:50 +00:00
83e1454a11
Added a method to determine the fraction of a sequence that's taken up by the most frequent base.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@781 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 20:35:31 +00:00
bdf772f017
Added test for determining the fraction of a sequence that's taken up by the most frequent base (quick-and-dirty homopolymer testing).
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@780 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 20:35:08 +00:00
d61a5261c1
Better integration of reference-ordered data into the data sharding system.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@779 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 20:09:32 +00:00
0d58e4ccc9
-check original alignments for indels when computing mismatch score
...
-move logging to debug
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@778 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 19:55:42 +00:00
5f67914b08
Added loads of documentation.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@777 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 19:40:47 +00:00
1a9d5cea29
Added a method to reverse-complement a String object, preserving 'N' and '.' bases.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@776 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 19:39:39 +00:00
a687c6bc03
Added a method to refresh an NFS mount point (necessary to prevent NFS flakiness when running on the LSF farm.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@774 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 19:31:54 +00:00
324ef9cbd1
Test class for PathUtils.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@773 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 19:31:22 +00:00
8515247575
Adding some functions I keep reinventing, especially for testing purposes.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@772 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 19:30:44 +00:00
e6200fe5b5
don't ignore reads when maxReadLength isn't set
...
also, print out LOD score for cleaning
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@771 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 19:24:10 +00:00
0219d33e10
QualityUtils: added reverse function to reverse an array of bytes (and not complement it), BaseUtils: split qualToProb into itself and qualToErrProb, CovariateCounterWalker and LogisticRecalibrationWalker: several changes including a properly acocunting (only partly complete) for reversing AND complementing bases that are negative strand, PrintReadsWalker: created option to output reads to a BAM file rather than just to the sceern (useful for creating a downsampled BAM file)
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@770 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 18:30:45 +00:00
7e77c62b49
auxiliary class, a simple struct to keep together info like numbers of covered, assessed, ref/variant bases across the sample
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@769 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 16:30:16 +00:00
7e5e422591
ReferenceOrdereData now inspects the ROD class using reflection. If the ROD declares a static Iterator<ROD> createIterator(String rodName, File rodFile) factory method, it is wrapped and used by the ReferenceOrderedData to read records from rodFile. If the ROD does not provide such factory method, the old behavior is the default: ReferenceOrderedData uses its own simple default iterator to read the file line by line (assuming there is only one line per record/position).
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@768 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 15:23:22 +00:00
26dd3cd50e
Cleanup. Move filtering functions closer to where they're used.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@767 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 21:42:48 +00:00
e7a6f8cdc4
Removed evidence of a previous incarnation of data sharding.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@766 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 20:48:33 +00:00
3cad580655
Catch and rethrow the walker's required argument, so that command-line arguments will be displayed when the GATK throws an argument exception.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@765 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 19:17:16 +00:00
dc748d9c9c
Integrate more feedback on command-line argument system. Focus on help
...
formatter: separate required from optional but otherwise keep ordering
the same, reorder GATK arguments by usage.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@764 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 19:01:25 +00:00
34f9820299
update mapping quality score and edit distance attribute for reads when they are cleaned
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@763 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 17:51:31 +00:00
57918de753
add the @Requires for this walker
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@762 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 17:03:12 +00:00
747521c849
Fixed the simplest of typos.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@761 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 16:00:30 +00:00
e48078b476
Updated to reflect change to BasecallingReadModel constructor.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@760 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 15:43:26 +00:00
505f588768
Forgot to say that the mate is unmapped too. This is necessary to prevent SAM-JDK from yelling at me about an invalid SAM file.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@759 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 15:38:51 +00:00
96e73e496a
Delete deprecated old-school traversals.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@758 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 14:57:17 +00:00
b840dd1320
Added some code to change the instrumentation for tests.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@756 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 05:15:27 +00:00
6c5fbb988b
Now basecalls an entire read (both ends of the pair, barcode... everything) at once. After, RawRead and FourProbRead can be asked to return a specified subset (corresponding to the ranges specified for each end of the read.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@754 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 00:09:20 +00:00
e293d65ede
Refactored to allow the user to specify the range of cycles they wish to call. Simply specify a single range (i.e. '0-75') or two ranges ('0-75,76-151'). This allows single and paired-end read processing to coexist happily. Also implements annotation of an aligned bam file (which should hopefully fit in under two gigs now, but I'm waiting on a bug fix or a clarification from the Picard team.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@753 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 00:07:24 +00:00
08c9f4d86b
Renamed to BasecallingTrainer.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@752 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 00:03:46 +00:00
01a3cb27c7
@Required / @Allows flags for main arguments.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@751 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-19 23:26:17 +00:00
40dbc21df7
Moved ParseException to it's own file and made it public.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@750 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-19 14:42:44 +00:00
ff798fe483
Reintroduce support for interval-based traversals.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@749 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-18 22:54:18 +00:00
3441795d9c
better handling of edge cases (zero coverage, reference mistakes, etc.)
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@747 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-18 18:04:37 +00:00
7c615c8fb0
Some changes to the system for annotating a pre-aligned bam file. Doesn't fit within 2gigs.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@746 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-18 17:42:08 +00:00
a39c8839c8
print percentage sign!
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@745 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-18 14:38:20 +00:00
c10741e9f5
Rename TraverseLociByReference to TraverseLoci to represent its new function.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@743 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-18 01:31:57 +00:00
e6ce80c8e3
Fix for GSA-44...don't throw exception when user specifies -h.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@742 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-18 00:42:00 +00:00
d35e20ce21
Better error checking for missing .dict file.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@741 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 21:57:12 +00:00
7161b8f927
Disable support for short name values directly abutting their arguments.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@740 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 16:09:32 +00:00
d152c2b911
New GATKArgumentCollection caused a subtle bug with argument grouping and the help system. Fixed.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@738 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 14:54:25 +00:00
94e324b844
Write N for the alt allele when we're hom-ref.
...
Stop EM loop when we've converged (likelihood[t-1] == likelihood[t]).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@737 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 13:58:11 +00:00
bd53bc18f9
added new required annotations
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@736 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 12:24:06 +00:00
28bf7ec8ad
Aesthetic cleanup.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@735 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 04:09:23 +00:00
a0464633fd
Whoops. Changed denominator from reads to bases.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@734 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 03:42:25 +00:00
5d60efc498
Factored out some simple stats accumulation.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@733 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 03:37:57 +00:00
81fac73c01
LOD checks for normal and brute force versions
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@732 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 02:56:03 +00:00
527df6e57b
Massive speed-up, clean-up and tabular output.
...
This program is going to rule.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@731 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-16 16:52:40 +00:00
3b57a35009
don't be tricked by multiple read groups with the same sample id!
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@730 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-16 15:28:55 +00:00
947bac5cdc
vast speedup
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@729 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-16 15:27:58 +00:00
6f1559bd77
Cleaned up a bit. Added some documentation.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@728 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-15 21:22:24 +00:00
2c4de7b5c5
Switch TraverseByLoci over to new sharding system, and cleanup some code in passing read files along
...
the pathway from command line to traversal engine.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@727 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-15 21:02:12 +00:00
f33f3c0434
added LOD threshold for determining when to clean
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@725 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-15 20:23:59 +00:00
99d4ebc26d
Added functionality to return the final accumulator of a traversal, so external tools can get the result of a walker.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@724 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-15 20:20:27 +00:00
dae77bf14a
Fixed a typo in a comment.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@723 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-15 20:07:31 +00:00
bfc40f54f0
Nicer output when training off of perfect reads. Not that that works yet...
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@722 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-15 20:07:08 +00:00
d1f3000afa
bed-style output for IGV
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@721 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-15 17:58:44 +00:00
36db44620b
Improved output. Can optionally limit the number reads actually called.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@720 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-15 00:07:57 +00:00
7834b969b4
Better interface to the tabular ROD, now makes writing files easier. Also has corresponding test files
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@719 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 23:20:11 +00:00
50f32b7f61
Added a shard strategy for the reduce-by-interval traversals. Also fixed bugs that I found along the way.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@718 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 21:20:18 +00:00
0f8e6061b6
Simple interface improvements
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@717 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 21:08:09 +00:00
8e9e2f4502
Revised ROD system. Split the system in Basic type and interface. Enabled more control over rod accessing, including an initialize() function to fetch headers and other options from the file. Added general tabular rod, which has a named columns and supports a map<String,String> interface. Comes with shiny new Junit system for RODs. Also, added simple python script for accessing picard data.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@716 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 21:06:28 +00:00
67293168e7
Support periods in sequence names.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@715 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 20:17:57 +00:00
641afc4e76
fix a crash in the event that the input file has no read groups!
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@714 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 19:27:41 +00:00
d8c1b010f1
Fixing the naming of the function I checked in earlier.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@713 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 19:27:10 +00:00
5858f20902
Documentation.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@712 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 18:58:43 +00:00
68c9455c0f
Moved the base complement method to BaseUtils.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@711 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 18:57:48 +00:00
asivache
aaron
andrewk
ebanks
hanna
kiran
depristo
jmaguire
kcibul