Mark DePristo b707331332 Encrypt GATK AWS keys using the GATK private key, and decrypt as needed as a resource when uploading to AWS logs ... -- 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		2013-01-30 16:42:23 -05:00
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R	Fix a nasty bug in reading GATK reports with a single line	2012-09-10 20:14:13 -04:00
c	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
chainFiles	…
doc	…
java	Encrypt GATK AWS keys using the GATK private key, and decrypt as needed as a resource when uploading to AWS logs	2013-01-30 16:42:23 -05:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Remove the ability to package GATK/Queue Lite from the build system	2013-01-28 02:42:37 -05:00
perl	Split out contig names from Reference .fai file on white space (to support the GATK resource bundle's file human_g1k_v37.fasta.fai.gz, which does not use tab delimiters)	2012-06-07 16:56:32 -04:00
scala	Making metrics a required parameter in MarkDuplicates	2013-01-25 17:49:49 -05:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00