File Changes for hiram

v295_preview to v295_preview2 (2014-01-20 to 2014-01-27) v295

• src/hg/featureBits/featureBits.c
  • lines changed 2, context: html, text, full: html, text
    correctly recognize _alt as a haplotype for hg38 refs #11681
  • lines changed 2, context: html, text, full: html, text
    clarify the backslash argument usage refs #11681
  • lines changed 4, context: html, text, full: html, text
    gather in the diaspora of haplotype check routines and add hg38 haplotype recognition refs #11681
• src/hg/hgChroms/hgChroms.c
  • lines changed 2, context: html, text, full: html, text
    gather in the diaspora of haplotype check routines and add hg38 haplotype recognition refs #11681
• src/hg/hgSelect/hgSelect.c
  • lines changed 2, context: html, text, full: html, text
    gather in the diaspora of haplotype check routines and add hg38 haplotype recognition refs #11681
• src/hg/inc/lav.h
  • lines changed 33, context: html, text, full: html, text
    move common lav reading business into the library and fixup more lavToPsl bugs and add to lav testing refs #12502
• src/hg/lib/lav.c
  • lines changed 156, context: html, text, full: html, text
    move common lav reading business into the library and fixup more lavToPsl bugs and add to lav testing refs #12502
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    move common lav reading business into the library and fixup more lavToPsl bugs and add to lav testing refs #12502
• src/hg/makeDb/doc/hg19.txt
  • lines changed 28, context: html, text, full: html, text
    update cosmic to v67 refs #10158
  • lines changed 28, context: html, text, full: html, text
    update cosmic to v67 refs #10158
• src/hg/makeDb/doc/hg38.txt
  • lines changed 87, context: html, text, full: html, text
    working up lineage specific repeats refs #11681
  • lines changed 28, context: html, text, full: html, text
    add ctgPos2 GRC Contigs track construction refs #11681
  • lines changed 17, context: html, text, full: html, text
    starting make downloads to be completed refs #11681
• src/hg/makeDb/trackDb/human/hg38/altSequences.ra
  • lines changed 20, context: html, text, full: html, text
    adding NCBI mappings next to UCSC mappings refs #11681
• src/hg/mouseStuff/axtFilter/axtFilter.c
  • lines changed 4, context: html, text, full: html, text
    gather in the diaspora of haplotype check routines and add hg38 haplotype recognition refs #11681
• src/hg/mouseStuff/chainFilter/chainFilter.c
  • lines changed 3, context: html, text, full: html, text
    gather in the diaspora of haplotype check routines and add hg38 haplotype recognition refs #11681
• src/hg/mouseStuff/chainNet/chainNet.c
  • lines changed 3, context: html, text, full: html, text
    gather in the diaspora of haplotype check routines and add hg38 haplotype recognition refs #11681
• src/hg/mouseStuff/chainPreNet/chainPreNet.c
  • lines changed 3, context: html, text, full: html, text
    gather in the diaspora of haplotype check routines and add hg38 haplotype recognition refs #11681
• src/hg/mouseStuff/lavToAxt/lavToAxt.c
  • lines changed 164, context: html, text, full: html, text
    move common lav reading business into the library and fixup more lavToPsl bugs and add to lav testing refs #12502
• src/hg/mouseStuff/lavToPsl/lavToPsl.c
  • lines changed 144, context: html, text, full: html, text
    move common lav reading business into the library and fixup more lavToPsl bugs and add to lav testing refs #12502
• src/hg/mouseStuff/lavToPsl/tests/input/hg19.chrom.sizes.gz
  • lines changed 0, context: html, text, full: html, text
    move common lav reading business into the library and fixup more lavToPsl bugs and add to lav testing refs #12502
• src/hg/mouseStuff/lavToPsl/tests/input/mm10.chrom.sizes.gz
  • lines changed 0, context: html, text, full: html, text
    move common lav reading business into the library and fixup more lavToPsl bugs and add to lav testing refs #12502
• src/hg/mouseStuff/lavToPsl/tests/input/trimEndsBug.lav
  • lines changed 35, context: html, text, full: html, text
    move common lav reading business into the library and fixup more lavToPsl bugs and add to lav testing refs #12502
• src/hg/mouseStuff/lavToPsl/tests/makefile
  • lines changed 66, context: html, text, full: html, text
    move common lav reading business into the library and fixup more lavToPsl bugs and add to lav testing refs #12502
• src/hg/mouseStuff/netFilter/netFilter.c
  • lines changed 3, context: html, text, full: html, text
    gather in the diaspora of haplotype check routines and add hg38 haplotype recognition refs #11681
• src/hg/utils/automation/makeDownloads.pl
  • lines changed 1, context: html, text, full: html, text
    gather in the diaspora of haplotype check routines and add hg38 haplotype recognition refs #11681
• src/inc/common.h
  • lines changed 4, context: html, text, full: html, text
    gather in the diaspora of haplotype check routines and add hg38 haplotype recognition refs #11681
• src/lib/common.c
  • lines changed 9, context: html, text, full: html, text
    gather in the diaspora of haplotype check routines and add hg38 haplotype recognition refs #11681
• src/product/scripts/trashCleanMonitor.sh
  • lines changed 1, context: html, text, full: html, text
    pass along SCRIPTS in scriptsDir refs #12540
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v295 preview2 refs #12352