GitHub PushEvent at 2014-02-21 21:54:25
Repository: adam
Actor: heuermh
Payload: {"shas":[["94bf2c06dfd8a7c53132faf6e2598cd0536fb3d5","1b7fbefd792d7a9793d7aac527d8c759c32763c6@alumni.stanford.edu","Adding ability to convert reference FASTA files for nucleotide sequences.","Frank Austin Nothaft",true],["515d7063c1c79391cfd9a99a560e8f6da7bb5067","de187642e6c75f60d10f29e52cab54cdf676870d@yeksigian.com","Merge pull request #79 from bigdatagenomics/fasta\n\nAdding ability to convert reference FASTA files for nucleotide sequences","Carl Yeksigian",true],["944d271e5c7b5f7fded4199e2856970a8fb90099","1b7fbefd792d7a9793d7aac527d8c759c32763c6@alumni.stanford.edu","Cleaning up variant context code to ease conversion.","Frank Austin Nothaft",true],["1da121bf021c27dd68380125925814cede3bc4b0","7841830342f748a54814a395669113bed0a8f742@cs.berkeley.edu","Add initial documentation on contributing","Matt Massie",true],["e023bca8f494349b7ed3550755a9dbc51f1fc5c5","1b7fbefd792d7a9793d7aac527d8c759c32763c6@berkeley.edu","Merge pull request #105 from bigdatagenomics/matt-contributing\n\nAdd initial documentation on contributing","Frank Austin Nothaft",true],["078f34d9ef3eb1b8907cdb9651d6dada2daa2980","9dcf5e33cfb31a2872893d1fd44fa7914cac0864@gmail.com","Encoding tag types in the ADAMRecord attributes, adding the 'tags' command.\n\nThis commit fixes issue 92 (https://github.com/bigdatagenomics/adam/issues/92).\n\nThe old style of encoding the \"optional fields\" from the SAM/BAM was to store\nthem as key=value pairs in the ADAMRecord.attributes string. However, this\nloses information about the _type_ of the tag/value, which is necessary if\nwe want to reconstruct the original value type (for example, for re-exporting\nBAM files from ADAM files).\n\nThis update is non-backwards-compatible, changing the format of the attributes\nfield to tag:type:value and introducing a new Attribute class for parsing and\nhandling these values.  It also adds functions to AdamRDDFunctions to allow for\nfiltering and subsetting of reads based on their tags, or to count the number of\ndistinct tags or tag-values across a set of reads.","Timothy Danford",true],["b23728f32292de4e13b7b36724829c2f4e966d98","1b7fbefd792d7a9793d7aac527d8c759c32763c6@berkeley.edu","Merge pull request #99 from genomebridge/attributeParser\n\nEncoding tag types in the ADAMRecord attributes, adding the 'tags' command","Frank Austin Nothaft",true],["bb61b421288b1ec3162ccd4333b33c8e645cfc91","1b7fbefd792d7a9793d7aac527d8c759c32763c6@alumni.stanford.edu","Cleaning up change documentation.","Frank Austin Nothaft",true],["af08968d90e6ab57f38ee98d558c22e72fc53073","9dcf5e33cfb31a2872893d1fd44fa7914cac0864@gmail.com","Merge pull request #107 from fnothaft/cleanup-change-docs\n\nCleaning up change documentation.","Timothy Danford",true],["c24c7dae2ec94e5647a1bc88fa3cc5310d1a78fb","9dcf5e33cfb31a2872893d1fd44fa7914cac0864@gmail.com","Added the spark.driver.port erasure to SparkFunSuite cleanup.\n\nWe've been getting intermittent errors, with respect to Spark being unable to bind to a port,\nin the context of repeated unit tests.  This apparently is a known problem, see the thread here:\n  http://blog.quantifind.com/posts/spark-unit-test/\nand the follow-up from Matei here:\n  https://groups.google.com/forum/#!topic/spark-users/MeVzgoJXm8I\n\nThe upshot is that we need to clearProperty('spark.driver.port') when we shut down our sparkContext\nafter a sparkTest.","Timothy Danford",true],["0957bdf6cbf4029208dd267a92731a64743d0319","1b7fbefd792d7a9793d7aac527d8c759c32763c6@berkeley.edu","Merge pull request #104 from genomebridge/tdanford/sparkfunsuite-port\n\nAdded the port erasure to SparkFunSuite's cleanup.","Frank Austin Nothaft",true],["5ee2d777610b360c3c6ffd1f1a9f8e131858be84","de187642e6c75f60d10f29e52cab54cdf676870d@yeksigian.com","New PluginExecutor command\n\n- A plugin class can be defined outside of the Adam jar, but run through\n  the normal AdamMain\n- An example plugin, the \"Take10Plugin\" is included in the test\n  directory\n- Adds a test suite to the cli module, which can reference the items\n  available in the core module\n- Adds notion of AccessControl to control the records which can be\n  accessed","Carl Yeksigian",true],["f7df24777f1c40d443e48c451947c2186c8f0ecf","de187642e6c75f60d10f29e52cab54cdf676870d@yeksigian.com","Build Fix & Changes for Frank's comments","Carl Yeksigian",true],["a20b21bd45143093bebfe47ed57415734c9426e9","de187642e6c75f60d10f29e52cab54cdf676870d@yeksigian.com","Revert change","Carl Yeksigian",true],["21f351c47b1b6da90c6ffbe2069360d569e255d4","de187642e6c75f60d10f29e52cab54cdf676870d@yeksigian.com","Updates for latest strand of comments\n\n- Functional test\n- More comments","Carl Yeksigian",true],["9db8da7f557031006f22e67cab3fffa0d583670b","7841830342f748a54814a395669113bed0a8f742@berkeley.edu","Merge pull request #108 from genomebridge/plugin\n\nAdding new PluginExecutor command","Matt Massie",true],["cb76a426c4d4bf821c396df03dabe16f38e7cc8b","9ca4d078a1a79adf8d1cc51e05561806957fbbf2@gmail.com","add fastq interleaver script","Jeremy Elson",true],["4a6b595ab1cacd56eada3ba24554feb72f3c4c47","de187642e6c75f60d10f29e52cab54cdf676870d@yeksigian.com","Add IRC Channel to readme","Carl Yeksigian",true],["0e01a4816dc46cf1be9f045a9a5b372de1a9bef5","1b7fbefd792d7a9793d7aac527d8c759c32763c6@berkeley.edu","Merge pull request #122 from genomebridge/irc-readme\n\nAdd IRC Channel to readme","Frank Austin Nothaft",true],["deaac9d7a86274547dfe28636ee8fa7db4495030","7841830342f748a54814a395669113bed0a8f742@cs.berkeley.edu","Add design doc to CONTRIBUTING document","Matt Massie",true]],"size":23,"ref":"refs/heads/master","head":"41068d94bda6075a7722b941d146c5df71fb3bcd"}