{"push_id":819083138,"size":5,"distinct_size":1,"ref":"refs/heads/ak_MeanQualityByCycle_spark2","head":"249e06aaaee0007b6c4b6bec889b1722ae6ffa46","before":"663d9762c6e9b5e912a13cdc72fd7b60f8e1c362","commits":[{"sha":"ac321f47f3a883e5dce0041a9bffc36b53403474","author":{"email":"96835dd8bfa718bd6447ccc87af89ae1675daeca@cloudera.com","name":"Tom White"},"message":"Add reference broadcasting to BQSR\n\nAdds a new file to LFS: human_g1k_v37.20.21.2bit. It was by applying the faToTwoBit binary from the \"kent\" UCSC utilities package on the similarly named fasta reference already in the repo.","distinct":false,"url":"https://api.github.com/repos/broadinstitute/hellbender/commits/ac321f47f3a883e5dce0041a9bffc36b53403474"},{"sha":"a4cadc361d2a42ae17a759b4c52b3fc7296bda4a","author":{"email":"1d0c6f32bb65b8defcf996a778a48a2d5cfb7c64@broadinstitute.org","name":"droazen"},"message":"Merge pull request #928 from broadinstitute/tw_ul_spark_bqsr\n\nAdd reference broadcasting to BQSR","distinct":false,"url":"https://api.github.com/repos/broadinstitute/hellbender/commits/a4cadc361d2a42ae17a759b4c52b3fc7296bda4a"},{"sha":"7733c1f62c227f8097bc4e7e9ff64231b4a6ba59","author":{"email":"1d0c6f32bb65b8defcf996a778a48a2d5cfb7c64@broadinstitute.org","name":"David Roazen"},"message":"GATKSparkTool: first step towards unifying handling of standard tool inputs in Spark\n\n-Created a new base class for Spark tools, GATKSparkTool, that centrally manages\n and validates standard tool inputs (reads, reference, and intervals). This allows\n us to enforce consistency across tools, delete duplicated boilerplate code from tools\n to load inputs, and perform standard kinds of validation (eg., sequence dictionary\n validation) in one place.\n\n-Tools that don't fit into the pattern established by GATKSparkTool can still extend\n SparkCommandLineProgram directly.\n\n-This is just a first step -- there is still much work to be done to unify our data source\n classes and transparently handle inputs from different sources (GCS, hdfs, files), but\n having inputs centrally managed should make the remaining tasks much easier.","distinct":false,"url":"https://api.github.com/repos/broadinstitute/hellbender/commits/7733c1f62c227f8097bc4e7e9ff64231b4a6ba59"},{"sha":"3e4357b3d4dcfc617c8e063bc9919d07955d2229","author":{"email":"1d0c6f32bb65b8defcf996a778a48a2d5cfb7c64@broadinstitute.org","name":"droazen"},"message":"Merge pull request #955 from broadinstitute/dr_gatksparktool\n\nGATKSparkTool: first step towards unifying handling of standard tool inputs in Spark","distinct":false,"url":"https://api.github.com/repos/broadinstitute/hellbender/commits/3e4357b3d4dcfc617c8e063bc9919d07955d2229"},{"sha":"249e06aaaee0007b6c4b6bec889b1722ae6ffa46","author":{"email":"ecd0cbdfcd6b30ea054daacf5620399c0b45c15b@gmail.com","name":"Adam Kiezun"},"message":"MeanQualityByCycle in Spark","distinct":true,"url":"https://api.github.com/repos/broadinstitute/hellbender/commits/249e06aaaee0007b6c4b6bec889b1722ae6ffa46"}]}