markd: changes by file

branch to review (2009-07-21 to 2009-07-27) v211

• src/hg/lib/hdb.c
  • 1.407 lines changed: 27, context: html, text, full: html, text
    reintroduced silent truncation of chromosome part of split table names as other code relies on the buggy behavior
• src/hg/makeDb/doc/anoCar1.txt
  • 1.21 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/bosTau4.txt
  • 1.17 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/calJac1.txt
  • 1.19 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/canFam2.txt
  • 1.21 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/cavPor3.txt
  • 1.19 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/danRer5.txt
  • 1.16 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/dasNov1.txt
  • 1.7 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/echTel1.txt
  • 1.6 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/equCab2.txt
  • 1.27 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/felCat3.txt
  • 1.54 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/fr2.txt
  • 1.23 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/galGal3.txt
  • 1.29 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/gasAcu1.txt
  • 1.37 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/hg18.txt
  • 1.370 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/hg19.txt
  • 1.31 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/loxAfr1.txt
  • 1.8 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/mm9.txt
  • 1.102 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/monDom5.txt
  • 1.13 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/ornAna1.txt
  • 1.26 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/oryCun1.txt
  • 1.9 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/oryLat2.txt
  • 1.13 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/otoGar1.txt
  • 1.9 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/panTro2.txt
  • 1.15 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/petMar1.txt
  • 1.21 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/ponAbe2.txt
  • 1.21 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/rheMac2.txt
  • 1.17 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/rn4.txt
  • 1.33 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/taeGut1.txt
  • 1.18 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/tetNig1.txt
  • 1.19 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/makeDb/doc/xenTro2.txt
  • 1.14 lines changed: 9, context: html, text, full: html, text
    added transmap update blurb
• src/hg/overlapSelect/chromAnn.c
  • 1.14 lines changed: 36, context: html, text, full: html, text
    fixed bug when doing stranded overlap with psls
• src/hg/overlapSelect/overlapSelect.c
  • 1.41 lines changed: 1, context: html, text, full: html, text
    fixed bug when doing stranded overlap with psls
• src/hg/overlapSelect/tests/makefile
  • 1.32 lines changed: 6, context: html, text, full: html, text
    fixed bug when doing stranded overlap with psls
• src/hg/overlapSelect/tests/expected/orthoStrandTest.stats
  • 1.1 lines changed: 2, context: html, text, full: html, text
    fixed bug when doing stranded overlap with psls
• src/hg/overlapSelect/tests/input/orthoIn.gp
  • 1.1 lines changed: 1, context: html, text, full: html, text
    fixed bug when doing stranded overlap with psls
• src/hg/overlapSelect/tests/input/orthoSel.psl
  • 1.1 lines changed: 1, context: html, text, full: html, text
    fixed bug when doing stranded overlap with psls
• src/hg/ratStuff/mafSpeciesList/mafSpeciesList.c
  • 1.2 lines changed: 7, context: html, text, full: html, text
    fixed memoryleak. remove chrom name from component names (from stanford)
• src/hg/ratStuff/mafsInRegion/mafsInRegion.c
  • 1.7 lines changed: 5, context: html, text, full: html, text
    added option to keep initial/training gaps in alignment'
  • 1.6 lines changed: 17, context: html, text, full: html, text
    fixed major memory leak (from stanford)
• src/lib/maf.c
  • 1.40 lines changed: 0, context: html, text, full: html, text
    fixed broken indent
  • 1.39 lines changed: 4, context: html, text, full: html, text
    fixed null pointer derefernces on i and e lines (from stanford); fix broken formatting
• src/lib/obscure.c
  • 1.47 lines changed: 2, context: html, text, full: html, text
    changed shuffleArrayOfPointer to produce a truly uniform random permutation of the input elements (from stanford)
• src/parasol/paraHub/paraHub.c
  • 1.130 lines changed: 1, context: html, text, full: html, text
    host names should be treated as case-insensitive (fix from stanford)