markd: changes by commit

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

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