File Changes for max

v365_preview2 to v365_base (2018-04-30 to 2018-05-07) v365

• src/hg/cirm/cdw/README
  • lines changed 6, context: html, text, full: html, text
    66a10b319053c2c36e8a6764e67ed8d907044e3a Wed May 2 17:06:39 2018 -0700
    CIRM: adding the daemon startup scripts to the repo, together with my modifications that rsync the genome onto the ramdisk, refs #21391
• src/hg/cirm/cdw/cdwMakePairedEndQa/cdwMakePairedEndQa.c
  • lines changed 75, context: html, text, full: html, text
    bc31d558a196fd4444c03309ec24b1d907cadd2b Wed May 2 12:27:06 2018 -0700
    CIRM: moving from BWA to bowtie as the workhose aligner for the QC data. A comment in cdwLib.c explains the motives. I had tried bwa aln, bwa mem, bowtie 1 and 2 and bowtie 1 was the best compromise between RAM consumption, runtime and compatibility with our existing bwa aln pipeline. refs #21391
• src/hg/cirm/cdw/cdwMakeRepeatQa/cdwMakeRepeatQa.c
  • lines changed 12, context: html, text, full: html, text
    bc31d558a196fd4444c03309ec24b1d907cadd2b Wed May 2 12:27:06 2018 -0700
    CIRM: moving from BWA to bowtie as the workhose aligner for the QC data. A comment in cdwLib.c explains the motives. I had tried bwa aln, bwa mem, bowtie 1 and 2 and bowtie 1 was the best compromise between RAM consumption, runtime and compatibility with our existing bwa aln pipeline. refs #21391
• src/hg/cirm/cdw/inc/cdwLib.h
  • lines changed 2, context: html, text, full: html, text
    bc31d558a196fd4444c03309ec24b1d907cadd2b Wed May 2 12:27:06 2018 -0700
    CIRM: moving from BWA to bowtie as the workhose aligner for the QC data. A comment in cdwLib.c explains the motives. I had tried bwa aln, bwa mem, bowtie 1 and 2 and bowtie 1 was the best compromise between RAM consumption, runtime and compatibility with our existing bwa aln pipeline. refs #21391
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 31, context: html, text, full: html, text
    bc31d558a196fd4444c03309ec24b1d907cadd2b Wed May 2 12:27:06 2018 -0700
    CIRM: moving from BWA to bowtie as the workhose aligner for the QC data. A comment in cdwLib.c explains the motives. I had tried bwa aln, bwa mem, bowtie 1 and 2 and bowtie 1 was the best compromise between RAM consumption, runtime and compatibility with our existing bwa aln pipeline. refs #21391
• src/hg/cirm/cdw/restartDaemons/cirm01-restartDaemons
  • lines changed 11, context: html, text, full: html, text
    66a10b319053c2c36e8a6764e67ed8d907044e3a Wed May 2 17:06:39 2018 -0700
    CIRM: adding the daemon startup scripts to the repo, together with my modifications that rsync the genome onto the ramdisk, refs #21391
• src/hg/cirm/cdw/restartDaemons/hgwdev-restartDaemons
  • lines changed 16, context: html, text, full: html, text
    66a10b319053c2c36e8a6764e67ed8d907044e3a Wed May 2 17:06:39 2018 -0700
    CIRM: adding the daemon startup scripts to the repo, together with my modifications that rsync the genome onto the ramdisk, refs #21391
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    912d19305d35c621b06ec6a8994ffb03c36105f0 Wed May 2 17:14:37 2018 -0700
    tweaking phegeni tdb, refs #21052