e50ae97fe1
Introduce new index-based fasta reader. Clean up MicroManager code, pushing necessary code back into TraversalEngine.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@531 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 19:40:21 +00:00
bd4cacb832
Added code to make a read group and sample name for BAM files that don't annotate them on reads. The defaults for both are now the filename, but this may be shortened in the future.
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The sample name for a read can be retrieved with the command:
read.getAttribute(SAMTag.RG.toString());
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@518 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 00:31:00 +00:00
635bfd8604
Added a little bit of hack to get the header back to the walker by initialization time, which was before sharding in the last version.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@516 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 21:07:11 +00:00
3dc2afd7ab
Added the ability to get a merged header in a LociByReference traversal
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@514 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 20:34:52 +00:00
3d7575bbb8
Oops...omitted walker.initialize().
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@504 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 17:35:28 +00:00
1bf4d040d8
Increase default shard size from 5 to 100000.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@494 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 18:29:44 +00:00
cb2f621d01
reverting accidental commit of change to shard size
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@490 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 00:33:28 +00:00
b820130dce
* added ability to load multiple BAM files from command line
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@489 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 00:28:08 +00:00
180ff13290
Added a bunch of changes to support the new MicroManager code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@431 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 18:29:38 +00:00
6db9127f90
Added changes to shattering, refactored SAMBAM into SAM
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@426 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 13:52:56 +00:00
0629f79049
Moved fasta support files into their own package.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@408 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 18:13:23 +00:00
c2669021b8
Cleanup, and support either by-interval traversals or full traversals in data source-backed code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@362 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-10 22:09:01 +00:00
2322bb7d86
Workaround: use a single ReferenceIterator for an entire micromanaged traversal. We'll have to
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do something about ReferenceIterator thread safety later.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@361 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-10 20:50:28 +00:00
8a1207e4db
Bringing up scaffolding for integration of locus traversals by reference with Aaron's data source code.
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Reverts to original TraverseByLociByReference behavior unless a special combination of command-line flags are used.
Lightly tested at best, and major flaws include:
- MicroManager is not doing MicroScheduling right now; it's driving the traversals.
- New database-ish data providers imply by their interface that they're stateless, but they're highly stateful.
- Using static objects to circumvent encapsulation.
- Code duplication is rampant.
- Plus more!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@346 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 20:28:17 +00:00
cfee59e0e6
New type hierarchy for Traversals. There's a new package to hold them (traversals) and an easy system to create new ones. We are now one step closer to supporting the execution manager (a totally non-functional version is included here) that actually executes walkers in parallel using N threads.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@214 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-27 15:40:45 +00:00
hanna
aaron
kcibul
depristo