markd: changes by file

review to branch (2009-07-27 to 2009-08-04) v212

• src/hg/hgTracks/makefile
  • 1.86 lines changed: 1, context: html, text, full: html, text
    allow more flexability in find SAMTools
• src/hg/hgc/makefile
  • 1.63 lines changed: 1, context: html, text, full: html, text
    allow more flexability in find SAMTools
• src/hg/lib/makefile
  • 1.393 lines changed: 5, context: html, text, full: html, text
    allow more flexability in find SAMTools
• src/hg/makeDb/doc/hg18.txt
  • 1.374 lines changed: 18, context: html, text, full: html, text
    added RNA Binding proteins track
• src/hg/makeDb/genbank/src/copy/gbMakeDownload
  • 1.21 lines changed: 25, context: html, text, full: html, text
    fixed time overflow check
  • 1.20 lines changed: 24, context: html, text, full: html, text
    added debugging for download build problem
• src/hg/maskOutFa/maskOutFa.c
  • 1.10 lines changed: 39, context: html, text, full: html, text
    add option to specify mask input format when reading from stdin. check command line options
• src/hg/mouseStuff/netFilter/netFilter.c
  • 1.23 lines changed: 17, context: html, text, full: html, text
    made several hard-coded parameters into command line options
  • 1.22 lines changed: 4, context: html, text, full: html, text
    added comment about how syntenic filtering works
• src/hg/overlapSelect/chromAnn.c
  • 1.15 lines changed: 2, context: html, text, full: html, text
    added rcsids
• src/hg/overlapSelect/chromAnnMap.c
  • 1.2 lines changed: 2, context: html, text, full: html, text
    added rcsids
• src/hg/overlapSelect/coordCols.c
  • 1.3 lines changed: 2, context: html, text, full: html, text
    added rcsids
• src/hg/overlapSelect/makefile
  • 1.14 lines changed: 1, context: html, text, full: html, text
    clean up executable
• src/hg/overlapSelect/overlapSelect.c
  • 1.42 lines changed: 2, context: html, text, full: html, text
    added rcsids
• src/hg/overlapSelect/rowReader.c
  • 1.5 lines changed: 2, context: html, text, full: html, text
    added rcsids
• src/hg/overlapSelect/selectTable.c
  • 1.31 lines changed: 2, context: html, text, full: html, text
    added rcsids
• src/hg/overlapSelect/tests/makefile
  • 1.34 lines changed: 1, context: html, text, full: html, text
    added new valgrid defs
  • 1.33 lines changed: 25, context: html, text, full: html, text
    added some test cases around strand
• src/hg/overlapSelect/tests/expected/xenoGpPslStatsStrandTest.stats
  • 1.1 lines changed: 7, context: html, text, full: html, text
    added some test cases around strand
• src/hg/overlapSelect/tests/expected/xenoPslGpStatsStrandTest.stats
  • 1.1 lines changed: 7, context: html, text, full: html, text
    added some test cases around strand
• src/hg/overlapSelect/tests/expected/xenoPslStatsStrandTest.stats
  • 1.1 lines changed: 7, context: html, text, full: html, text
    added some test cases around strand
• src/hg/overlapSelect/tests/expected/xenoPslStatsTest.stats
  • 1.1 lines changed: 13, context: html, text, full: html, text
    added some test cases around strand
• src/hg/overlapSelect/tests/input/xenoEst1.gp
  • 1.1 lines changed: 5, context: html, text, full: html, text
    forgot test file
• src/hg/overlapSelect/tests/input/xenoEst1.psl
  • 1.1 lines changed: 5, context: html, text, full: html, text
    added some test cases around strand
• src/hg/ratStuff/mafSplitPos/mafSplitPos.c
  • 1.7 lines changed: 8, context: html, text, full: html, text
    allow disabling gap or repeat spliting, fixed bug creating duplicate output, make -minRepeat actually work
• src/inc/common.mk
  • 1.65 lines changed: 10, context: html, text, full: html, text
    allow more flexability in find SAMTools
• src/utils/faCount/faCount.c
  • 1.8 lines changed: 99, context: html, text, full: html, text
    Add options for counting di-nucleotide frequencies and looking at both strands of the input sequences. (from stanford)