- ReduceReads by default now sets up-front ReadWalker downsampling to 40x per start position.
- This is the value I used in my tests with Picard to show that memory issues pretty much disappeared.
- This should hopefully take care of the memory issues being reported on the forum.
- Added javadocs to SlidingWindow (the main RR class) to follow GATK conventions.
- Added more unit tests to increase coverage of BaseCounts class.
- Added more unit tests to test I/D operators in the SlidingWindow class.
-- This is a good idea in case the key that's provided to the GATK doesn't have an appropriately restrictive access policy, and could actually delete objects, or list the bucket(s). With this unit test we know that the public distributed key cannot do too much damage
-- Bringing code up to document, style, and code coverage specs
-- Move GATKRunReportUnitTest to private
-- Fully expand GATKRunReportUnitTests to coverage writing and reading GATKRunReport to local disk, to standard out, to AWS.
-- Move documentation URL from GATKRunReport to UserException
-- Delete a few unused files from s3GATKReport
-- Added capabilities to GATKRunReport to make testing easier
-- Added capabilities to deserialize GATKRunReports from an InputStream
-- Moved all scripts, data files, and python programs into private/GATKLogs
-- Updated the AWS user creation script to make two derived users: GATK2LogUploader and GATK2LogDownloader with new keys. I'll roll these out in subsequent commit.
- Added RR qual correctness tests (note that this is a case where we don't add code coverage but still need to test critical infrastructure).
- Also added minor cleanup of BaseUtils
I've confirmed via a script that all of these differences only
involve the version number bump in the BAM headers and nothing
else:
< @HD VN:1.0 GO:none SO:coordinate
---
> @HD VN:1.4 GO:none SO:coordinate
These patches to GATKBAMIndex are causing massive BAM index reading errors in
combination with the latest version of Picard. The bug is either in the patches
themselves or in the underlying SeekableBufferedStream class they rely on. Until
the cause can be identified, we are temporarily backing out these changes so that
we can continue to run with the latest Picard/Tribble.
This reverts commits:
81483ec21e528790dfa719d18cdee27d577ca98e
68cf0309db490b79eecdabb4034987ff825ffea8
54bb68f28ad5fe1b3df01702e9c5e108106a0176
This is a necessary prerequisite for the org.broadinstitute.variant migration.
-Picard and sam-jdk go from version 1.67.1197 to 1.84.1337
-Picard-private goes from version 2375 to 2662
-Tribble goes from version 119 to 1.84.1337
-RADICALLY trimmed down the list of classes we extract from Picard-private
(jar goes from 326993 bytes to 6445 bytes!)
I've confirmed via a script that all of these differences only
involve the version number bump in the BAM headers and nothing
else:
< @HD VN:1.0 GO:none SO:coordinate
---
> @HD VN:1.4 GO:none SO:coordinate
These patches to GATKBAMIndex are causing massive BAM index reading errors in
combination with the latest version of Picard. The bug is either in the patches
themselves or in the underlying SeekableBufferedStream class they rely on. Until
the cause can be identified, we are temporarily backing out these changes so that
we can continue to run with the latest Picard/Tribble.
This reverts commits:
81483ec21e528790dfa719d18cdee27d577ca98e
68cf0309db490b79eecdabb4034987ff825ffea8
54bb68f28ad5fe1b3df01702e9c5e108106a0176
This is a necessary prerequisite for the org.broadinstitute.variant migration.
-Picard and sam-jdk go from version 1.67.1197 to 1.84.1337
-Picard-private goes from version 2375 to 2662
-Tribble goes from version 119 to 1.84.1337
-RADICALLY trimmed down the list of classes we extract from Picard-private
(jar goes from 326993 bytes to 6445 bytes!)
Resources must be in a subdirectory called "resources" in the package
hierarchy to be picked up by the packaging system. Adding each resource
manually to the jars in build.xml does not cause the resource to be
added to the standalone GATK jar when we package the GATK, so it's best
to always use this convention.
If a read had an existing BAQ tag, was clipped by our engine, and couldn't have the BAQ recalculated (for whatever reason), then we would
fail in the BQSR because we would default to using the old tag (which no longer matched the length of the read bases).
The right thing to do here is to remove the old BAQ tag when RECALCULATE and ADD_TAG are the BAQ modes used but BAQ cannot be recalculated.
Added a unit test to ensure that the tags are removed in such a case.
testing the adding of reads into the SlidingWindow plus consensus creation. Will flesh these out more after I take care of
some other items on my plate.
-- Has the overall effect that the GATK user AWS keys are no longer visible in the gatk source as plain text. This will stop AWS from emailing me (they crawl the web looking for keys)
-- Added utility EncryptAWSKeys that takes as command line arguments the GATK user AWS access and secret keys, encrypts them with the GATK private key, and writes out the resulting file to resources in phonehome.
-- GATKRunReport now decrypts as needed these keys using the GATK public key as resources in the GATK bundle
-- Refactored the essential function of Resource (reading the resource) from IOUtils into the class itself. Now how to get the data in the resouce is straightforward
-- Refactored md5 calculation code from a byte[] into Utils. Added unit tests
-- Committing the encrypted AWS keys
-- #resolves https://jira.broadinstitute.org/browse/GSA-730
Eric Banks
Guillermo del Angel
Mark DePristo
Ryan Poplin
David Roazen
Ami Levy-Moonshine