Commits for hiram

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

• update cosmic to v67 refs #10158
  • src/hg/makeDb/doc/hg19.txt - lines changed 28, context: html, text, full: html, text
• update cosmic to v67 refs #10158
  • src/hg/makeDb/doc/hg19.txt - lines changed 28, context: html, text, full: html, text
• working up lineage specific repeats refs #11681
  • src/hg/makeDb/doc/hg38.txt - lines changed 87, context: html, text, full: html, text
• pass along SCRIPTS in scriptsDir refs #12540
  • src/product/scripts/trashCleanMonitor.sh - lines changed 1, context: html, text, full: html, text
• add ctgPos2 GRC Contigs track construction refs #11681
  • src/hg/makeDb/doc/hg38.txt - lines changed 28, context: html, text, full: html, text
• correctly recognize _alt as a haplotype for hg38 refs #11681
  • src/hg/featureBits/featureBits.c - lines changed 2, context: html, text, full: html, text
• clarify the backslash argument usage refs #11681
  • src/hg/featureBits/featureBits.c - lines changed 2, context: html, text, full: html, text
• starting make downloads to be completed refs #11681
  • src/hg/makeDb/doc/hg38.txt - lines changed 17, context: html, text, full: html, text
• adding NCBI mappings next to UCSC mappings refs #11681
  • src/hg/makeDb/trackDb/human/hg38/altSequences.ra - lines changed 20, context: html, text, full: html, text
• gather in the diaspora of haplotype check routines and add hg38 haplotype recognition refs #11681
  • src/hg/featureBits/featureBits.c - lines changed 4, context: html, text, full: html, text
  • src/hg/hgChroms/hgChroms.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hgSelect/hgSelect.c - lines changed 2, context: html, text, full: html, text
  • src/hg/mouseStuff/axtFilter/axtFilter.c - lines changed 4, context: html, text, full: html, text
  • src/hg/mouseStuff/chainFilter/chainFilter.c - lines changed 3, context: html, text, full: html, text
  • src/hg/mouseStuff/chainNet/chainNet.c - lines changed 3, context: html, text, full: html, text
  • src/hg/mouseStuff/chainPreNet/chainPreNet.c - lines changed 3, context: html, text, full: html, text
  • src/hg/mouseStuff/netFilter/netFilter.c - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/automation/makeDownloads.pl - lines changed 1, context: html, text, full: html, text
  • src/inc/common.h - lines changed 4, context: html, text, full: html, text
  • src/lib/common.c - lines changed 9, 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/inc/lav.h - lines changed 33, context: html, text, full: html, text
  • src/hg/lib/lav.c - lines changed 156, context: html, text, full: html, text
  • src/hg/lib/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/mouseStuff/lavToAxt/lavToAxt.c - lines changed 164, context: html, text, full: html, text
  • src/hg/mouseStuff/lavToPsl/lavToPsl.c - lines changed 144, context: html, text, full: html, text
  • src/hg/mouseStuff/lavToPsl/tests/input/trimEndsBug.lav - lines changed 35, context: html, text, full: html, text
  • 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/lavToPsl/tests/input/hg19.chrom.sizes.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/mouseStuff/lavToPsl/tests/input/mm10.chrom.sizes.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• v295 preview2 refs #12352
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text