Commits for braney

v295_base to v296_preview (2014-02-03 to 2014-02-10) v296

• fix a bug in how lineFile deals with the udc cache.
  • src/lib/linefile.c - lines changed 2, context: html, text, full: html, text
• change %i to %d in response to code review
  • src/utils/bigWigCat/bigWigCat.c - lines changed 2, context: html, text, full: html, text
• fix up hg38
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 3, context: html, text, full: html, text
• fix crash in multiWig if underlying bigWig file was not found
  • src/hg/hgTracks/multiWig.c - lines changed 3, context: html, text, full: html, text
• fix a problem with maf's that are read from stdin, in which case wedon't want to use udc. Probably we should get udc to work with stdin.
  
  • src/lib/maf.c - lines changed 7, context: html, text, full: html, text
• fix problem of disappearing narrow peak discussed in #12558 bynormalizing the statics to reflect that base counts are integers.
  
  • src/lib/bbiRead.c - lines changed 37, context: html, text, full: html, text
• update the test output that depends on bigWigSummary output which haschanged ever so slightly as a result of a fix made to how statistics are
  calculated in the bigWig summary calculations
  
  • src/utils/bigWigCat/tests/expected/tbg1.sum - lines changed 1, context: html, text, full: html, text
  • src/utils/bigWigCat/tests/expected/tbg10.sum - lines changed 1, context: html, text, full: html, text
  • src/utils/bigWigCat/tests/expected/tbg100.sum - lines changed 1, context: html, text, full: html, text
  • src/utils/bigWigCat/tests/expected/tbg1000.sum - lines changed 1, context: html, text, full: html, text
  • src/utils/bigWigCat/tests/expected/tbg10000.sum - lines changed 1, context: html, text, full: html, text
  • src/utils/bigWigCat/tests/expected/tf1.sum - lines changed 1, context: html, text, full: html, text
  • src/utils/bigWigCat/tests/expected/tf10.sum - lines changed 1, context: html, text, full: html, text
  • src/utils/bigWigCat/tests/expected/tf3.sum - lines changed 1, context: html, text, full: html, text
  • src/utils/bigWigCat/tests/expected/tv1.sum - lines changed 1, context: html, text, full: html, text
  • src/utils/bigWigCat/tests/expected/tv10.sum - lines changed 1, context: html, text, full: html, text
  • src/utils/bigWigCat/tests/expected/tv100.sum - lines changed 1, context: html, text, full: html, text
  • src/utils/wigToBigWig/tests/expected/tf1.sum - lines changed 1, context: html, text, full: html, text
  • src/utils/wigToBigWig/tests/expected/tv1.sum - lines changed 1, context: html, text, full: html, text
  • src/utils/wigToBigWig/tests/expected_2/tbg1.sum - lines changed 1, context: html, text, full: html, text
  • src/utils/wigToBigWig/tests/expected_2/tbg10.sum - lines changed 1, context: html, text, full: html, text
  • src/utils/wigToBigWig/tests/expected_2/tbg100.sum - lines changed 1, context: html, text, full: html, text
  • src/utils/wigToBigWig/tests/expected_2/tbg1000.sum - lines changed 1, context: html, text, full: html, text
  • src/utils/wigToBigWig/tests/expected_2/tbg10000.sum - lines changed 1, context: html, text, full: html, text
  • src/utils/wigToBigWig/tests/expected_2/tf1.sum - lines changed 1, context: html, text, full: html, text
  • src/utils/wigToBigWig/tests/expected_2/tf10.sum - lines changed 1, context: html, text, full: html, text
  • src/utils/wigToBigWig/tests/expected_2/tf3.sum - lines changed 1, context: html, text, full: html, text
  • src/utils/wigToBigWig/tests/expected_2/tv1.sum - lines changed 1, context: html, text, full: html, text
  • src/utils/wigToBigWig/tests/expected_2/tv10.sum - lines changed 1, context: html, text, full: html, text
  • src/utils/wigToBigWig/tests/expected_2/tv100.sum - lines changed 1, context: html, text, full: html, text
• add hg38 to assemblies updated
  • src/hg/makeDb/genbank/etc/hgwdev.dbs - lines changed 1, context: html, text, full: html, text