markd: changes by file

branch to review (2009-04-14 to 2009-04-21) v204

• src/hg/makeDb/doc/taeGut1.txt
  • 1.16 lines changed: 30, context: html, text, full: html, text
    added taeGut1 N-SCAN
• src/hg/makeDb/genbank/doc/config.html
  • 1.24 lines changed: 11, context: html, text, full: html, text
    refactored alignment code to allow use of genome partitioning in other code. removed outdated iserver code
• src/hg/makeDb/genbank/etc/genbank.conf
  • 1.335 lines changed: 2, context: html, text, full: html, text
    refactored alignment code to allow use of genome partitioning in other code. removed outdated iserver code
• src/hg/makeDb/genbank/src/align/gbAlignIServerClean
  • 1.6 lines changed: 70, context: html, text, full: html, text
    refactored alignment code to allow use of genome partitioning in other code. removed outdated iserver code
• src/hg/makeDb/genbank/src/align/gbAlignIServerCopy
  • 1.5 lines changed: 90, context: html, text, full: html, text
    refactored alignment code to allow use of genome partitioning in other code. removed outdated iserver code
• src/hg/makeDb/genbank/src/align/gbAlignSetup
  • 1.24 lines changed: 175, context: html, text, full: html, text
    refactored alignment code to allow use of genome partitioning in other code. removed outdated iserver code
• src/hg/makeDb/genbank/src/align/gbAlignStep
  • 1.24 lines changed: 49, context: html, text, full: html, text
    refactored alignment code to allow use of genome partitioning in other code. removed outdated iserver code
• src/hg/makeDb/genbank/src/align/makefile
  • 1.9 lines changed: 2, context: html, text, full: html, text
    refactored alignment code to allow use of genome partitioning in other code. removed outdated iserver code
• src/hg/makeDb/genbank/src/dbload/gbAlignTbl.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    fix bug where mgc/orfeone psl tables were not updated when clones were deleted from MGC
• src/hg/makeDb/genbank/src/dbload/gbAlignTbl.h
  • 1.2 lines changed: 1, context: html, text, full: html, text
    fix bug where mgc/orfeone psl tables were not updated when clones were deleted from MGC
• src/hg/makeDb/genbank/src/dbload/gbMetaData.c
  • 1.48 lines changed: 13, context: html, text, full: html, text
    fix bug where mgc/orfeone psl tables were not updated when clones were deleted from MGC
• src/hg/makeDb/genbank/src/gbSanity/chkMetaDataTbls.c
  • 1.12 lines changed: 2, context: html, text, full: html, text
    fixed change on type of accession in refLink
• src/hg/makeDb/genbank/src/lib/gbCommon.pm
  • 1.41 lines changed: 8, context: html, text, full: html, text
    refactored alignment code to allow use of genome partitioning in other code. removed outdated iserver code
• src/hg/makeDb/genbank/src/lib/makefile
  • 1.7 lines changed: 1, context: html, text, full: html, text
    refactored alignment code to allow use of genome partitioning in other code. removed outdated iserver code
• src/hg/makeDb/genbank/src/lib/py/genbank/GenomePartition.py
  • 1.1 lines changed: 159, context: html, text, full: html, text
    refactored alignment code to allow use of genome partitioning in other code. removed outdated iserver code
• src/hg/makeDb/genbank/src/lib/py/genbank/GenomeSeqs.py
  • 1.4 lines changed: 29, context: html, text, full: html, text
    refactored alignment code to allow use of genome partitioning in other code. removed outdated iserver code
• src/hg/makeDb/genbank/src/lib/py/genbank/__init__.py
  • 1.3 lines changed: 5, context: html, text, full: html, text
    refactored alignment code to allow use of genome partitioning in other code. removed outdated iserver code
• src/hg/makeDb/trackDb/zebraFinch/nscanGene.html
  • 1.1 lines changed: 68, context: html, text, full: html, text
    added taeGut1 N-SCAN
• src/hg/makeDb/trackDb/zebraFinch/taeGut1/trackDb.ra
  • 1.2 lines changed: 8, context: html, text, full: html, text
    added taeGut1 N-SCAN
• src/hg/mouseStuff/lavToPsl/lavToPsl.c
  • 1.11 lines changed: 5, context: html, text, full: html, text
    fix bug with name when lastz input is a 2bit
• src/lib/tests/makefile
  • 1.34 lines changed: 6, context: html, text, full: html, text
    fixed test problem due to timing of processes
• src/lib/tests/expected/pipelineWriteErr.err
  • 1.3 lines changed: 2, context: html, text, full: html, text
    fixed test problem due to timing of processes