Commits for braney

v290_preview to v290_preview2 (2013-09-16 to 2013-09-23) v290

• add new option -maxAlignsDrop=N to pslCDnaFilter that drops all thealignments of a query that aligns more than N times.
  
  • src/hg/pslCDnaFilter/algo.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/pslCDnaFilter.c - lines changed 37, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/usage.txt - lines changed 4, context: html, text, full: html, text
• add an option to pslCDnaFilter to treat matches in repeats the same asmatches that aren't.
  
  • src/hg/pslCDnaFilter/cDnaAligns.h - lines changed 2, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/cDnaReader.c - lines changed 6, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/pslCDnaFilter.c - lines changed 3, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/usage.txt - lines changed 2, context: html, text, full: html, text
• code to support version numbers in *efSeg id's , and to support newfiltering regime that doesn't filter based on repeat content.
  
  • src/hg/hgTracks/simpleTracks.c - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/align.dbs - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/dbload/dbLoadOptions.h - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/dbload/dbLoadPartitions.c - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/dbload/gbAlignData.c - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/dbload/gbDbLoadStep - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/dbload/gbGeneTbl.c - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/dbload/gbGeneTbl.h - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/dbload/gbLoadRna.c - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/inc/gbDefs.h - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 1, context: html, text, full: html, text
• oops, a little fix to updating metadata to track whether to keep theversion #
  
  • src/hg/makeDb/genbank/src/dbload/gbMetaData.c - lines changed 5, context: html, text, full: html, text
• add more lines to this file ignore.idx which is a list of lines
  • src/hg/makeDb/genbank/etc/ignore.idx - lines changed 5, context: html, text, full: html, text