markd: changes by commit

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

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