File Changes for kent

v305_preview2 to v305_base (2014-08-25 to 2014-09-02) v305

• src/hg/encode3/eap/eapSchedule/eapSchedule.c
  • lines changed 8, context: html, text, full: html, text
    Removing sponge-force kludge and allowing hg38 to happen.
• src/hg/encode3/eap/inc/eapGraph.h
  • lines changed 1, context: html, text, full: html, text
    Fixing typo in comment.
• src/hg/encode3/eap/lib/eapGraph.c
  • lines changed 1, context: html, text, full: html, text
    Fixing typo in comment.
• src/hg/encode3/encodeDataWarehouse/edwMakeReplicateQa/edwMakeReplicateQa.c
  • lines changed 3, context: html, text, full: html, text
    Only doing replicate comparisons on same assembly.
• src/hg/oneShot/freen/freen.c
  • lines changed 226, context: html, text, full: html, text
    First cut of parallelizing seems to work.
  • lines changed 220, context: html, text, full: html, text
    Moving pthreadDoList to new library module, and the parallel hacTree to hacTree.c.
• src/inc/hacTree.h
  • lines changed 6, context: html, text, full: html, text
    Adding hacTreeMultiThread.
  • lines changed 18, context: html, text, full: html, text
    Adding possibility to include precalculated distances to hacTreeMultiThread and improving commenting.
  • lines changed 12, context: html, text, full: html, text
    Removing hacTreeExpensiveMerges and simplifying hacTreeMultiThread
• src/inc/pthreadDoList.h
  • lines changed 67, context: html, text, full: html, text
    Moving pthreadDoList to new library module, and the parallel hacTree to hacTree.c.
• src/lib/hacTree.c
  • lines changed 20, context: html, text, full: html, text
    Reversing ordering, and refactoring to set up for parallelization of distance calcs.
  • lines changed 126, context: html, text, full: html, text
    Moving pthreadDoList to new library module, and the parallel hacTree to hacTree.c.
  • lines changed 37, context: html, text, full: html, text
    Adding possibility to include precalculated distances to hacTreeMultiThread and improving commenting.
  • lines changed 15, context: html, text, full: html, text
    Changing the new hacTree code so that it creates trees in same order (I hope) as old code. Previously it was inverting some branches.
  • lines changed 198, context: html, text, full: html, text
    Removing hacTreeExpensiveMerges and simplifying hacTreeMultiThread
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Moving pthreadDoList to new library module, and the parallel hacTree to hacTree.c.
• src/lib/pthreadDoList.c
  • lines changed 109, context: html, text, full: html, text
    Moving pthreadDoList to new library module, and the parallel hacTree to hacTree.c.
  • lines changed 5, context: html, text, full: html, text
    Adding empty list short-cut and threadCount error checking.
• src/oneShot/bigWigCluster/bigWigCluster.c
  • lines changed 318, context: html, text, full: html, text
    Parallelized bigWig clustering via hacTree to produce a json graph seems to work.
  • lines changed 131, context: html, text, full: html, text
    Adding tabular output. Commenting and cleaning up code.
• src/oneShot/bigWigCluster/makefile
  • lines changed 3, context: html, text, full: html, text
    Parallelized bigWig clustering via hacTree to produce a json graph seems to work.
• src/oneShot/hacTreeTest/hacTreeTest.c
  • lines changed 118, context: html, text, full: html, text
    Adding a little test program.
• src/oneShot/hacTreeTest/makefile
  • lines changed 3, context: html, text, full: html, text
    Adding a little test program.
• src/oneShot/hacTreeTest/testIt
  • lines changed 3, context: html, text, full: html, text
    Adding a little test program.
• src/oneShot/orderMiddle/makefile
  • lines changed 7, context: html, text, full: html, text
    Moving utility that doesn't really work to oneShot.
• src/oneShot/orderMiddle/orderMiddle.c
  • lines changed 145, context: html, text, full: html, text
    Moving utility that doesn't really work to oneShot.
• src/oneShot/orderMiddle/test.expected
  • lines changed 6, context: html, text, full: html, text
    Moving utility that doesn't really work to oneShot.
• src/oneShot/orderMiddle/test.lst
  • lines changed 6, context: html, text, full: html, text
    Moving utility that doesn't really work to oneShot.
• src/oneShot/orderMiddle/test.pair
  • lines changed 15, context: html, text, full: html, text
    Moving utility that doesn't really work to oneShot.
• src/utils/bigWigCluster/bigWigCluster.c
  • lines changed 243, context: html, text, full: html, text
    Swapping in Jim's version which fixes some parallelization issues and adds a new tabular output.
• src/utils/bigWigCorrelate/bigWigCorrelate.c
  • lines changed 11, context: html, text, full: html, text
    Adding -rootNames option, and making by default system output complete input file name instead of just root name.
• src/utils/orderMiddle/makefile
  • lines changed 4, context: html, text, full: html, text
    Adding test target.
  • lines changed 7, context: html, text, full: html, text
    Moving utility that doesn't really work to oneShot.
• src/utils/orderMiddle/orderMiddle.c
  • lines changed 145, context: html, text, full: html, text
    Moving utility that doesn't really work to oneShot.
• src/utils/orderMiddle/test.expected
  • lines changed 6, context: html, text, full: html, text
    Moving utility that doesn't really work to oneShot.
• src/utils/orderMiddle/test.lst
  • lines changed 6, context: html, text, full: html, text
    Moving utility that doesn't really work to oneShot.
• src/utils/orderMiddle/test.pair
  • lines changed 15, context: html, text, full: html, text
    Moving utility that doesn't really work to oneShot.