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.
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GATK users from the readers, which they could abuse in ways that could destabilize the GATK.
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simplification of some of the locus traversal code.
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Now the IndelRealigner can use this functionality without being forced to merge abutting intervals (which was actually causing a problem with the cleaning).
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In indel cleaner:
1. allow the user to specify that he wants to use Picardâs SAMFileWriter sorting on disk instead of having us sort in memory; this is useful if the input consists of long reads.
2. for N-way-out mode: output bams now use the original headers from the corresponding input bams - as opposed to the merged header. This entailed some reworking of the datasources code.
3. intermediate check-in of code that allows user to input known indels to be used as alternate consenses. Not done yet.
In UG: fix bug in beagle output for Jared.
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2. Used said mapping to implement N-way-in,N-way-out functionality in the new indel cleaner. Still needs more testing (to be done after vacation but preliminary tests look good).
3. Fixes to VCF validator: ignore case when testing VCF reference base against true reference base and allow quals of -1 (as per spec).
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support batched intervals in a single shard, but intervals are not yet compressed into a single
shard.
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* Moved GATKArgumentCollection into gatk.arguments folder to clean up the main folder, also added some associated argument classes (most of the changes).
* Added code the argument parsing system for default enums, we needed this so we could preserve the current unsafe flag, and at the same time allow finer grained control of unsafe operations. You can now specify:
"-U" (for all unsafe operations), "-U ALLOW_UNINDEXED_BAM" (only allow unindexed BAMs), "-U NO_READ_ORDER_VERIFICATION", etc.
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1: all overlapping and abutting intervals merged (ALL),
2: just overlapping, not abutting intervals (OVERLAPPING_ONLY),
3: no merging (NONE). This option is not currently allowed, it will throw an exception. Once we're more certain that unmerged lists are going to work in all cases in the GATK, we'll enable that.
The command line option is --interval_merging or -im
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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.
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and displays walker data extracted from the JavaDoc. Needs a bit of help,
both in content and flexibility of package naming.
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Just stomped on the existing md5s because that's what Eric told me to do.
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Revert until we find out whether the cause is legit.
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The user is warned if a locus exceeds this threshold, and no more reads are added.
Also CombineDup walker had an incorrect package name.
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also fixed some verbage in the GAEngine.
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sources and post-construction validation back into the GATKEngine, leaving the MicroScheduler
to just microschedule.
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rough initial implementation, but should provide enough support so that people can stop
creating SAMFileWriters in reduceInit.
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inspecting the source tree and loading walkers, rather than trying to roll
our own by hand.
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depristo
aaron
hanna
ebanks
asivache
rpoplin
andrewk