b840dd1320
Added some code to change the instrumentation for tests.
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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.
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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.
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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.
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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.
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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.
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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.
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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.)
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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.
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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!
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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.
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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.
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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.
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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.
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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.
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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.
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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
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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.
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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.
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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.
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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
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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.
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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!
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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
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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.
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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
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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
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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.
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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.
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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...
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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
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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.
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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
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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.
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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
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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.
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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.
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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!
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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.
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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.
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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.
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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
3761c0900b
Added Bustard vs. Four-prob percent bases consistent output.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@710 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 18:01:41 +00:00
7a1f85ff86
option to print out the indels found by the cleaner to a file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@709 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 17:50:08 +00:00
b62bddee42
The header was never being set.
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Added this hack for now and will alert the authorities ASAP...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@708 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 17:18:51 +00:00
959cf09d4b
Removed some debugging print statements.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@707 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 17:12:42 +00:00
2f42a643a8
A new, much simpler (and now, complete) driver program for four-base probs. Serves as a model for anyone who wants to write their own driver program that trains and calls with data from a different source than the raw Illumina data.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@706 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:58:22 +00:00
5824dea0c1
Trains and calls a read at a time rather than a base at a time (which, given it's name, it should have done in the first place)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@705 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:57:00 +00:00
e4770885fd
The four-probs for all bases in a single read. Some utility functions for generating the primary and secondary base strings, as well as generating the SQ tag byte array in a manner that's consistent with the Bustard base calls (meaning the primary Bustard call and the secondary Four-Prob call are not permitted to be the same).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@704 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:55:49 +00:00
fdd123fe16
A parser the raw Illumina data. Allows one to arbitrarily jump from one tile to another.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@703 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:53:07 +00:00
7aa90757ac
Moved the iterators over to the StingSAMIterator interface. This will help us ensure that iterators that need to be closed get closed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@702 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:52:18 +00:00
aaron
kiran
hanna
jmaguire
asivache
kcibul
ebanks
depristo