Commits for hiram

v328_preview2 to v328_base (2016-01-25 to 2016-02-08) v328

• Gap= lines are on the cDNA_match lines not just match lines refs #13673
  
  • src/hg/utils/gff3ToPsl/gff3ToPsl.c - lines changed 1, context: html, text, full: html, text
• testing NCBI RefSeq track refs #13673
  
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 18, context: html, text, full: html, text
• testing NCBI RefSeq track refs #13673
  
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 8, context: html, text, full: html, text
• working up script for NCBI RefSeq gene track processing refs #13673
  
  • src/hg/utils/automation/doNcbiRefSeq.pl - lines changed 280, context: html, text, full: html, text
  • src/hg/utils/automation/gff3ToRefLink.pl - lines changed 359, context: html, text, full: html, text
• adding microsat track refs #15209
  
  • src/hg/makeDb/doc/ce11/initialBuild.txt - lines changed 11, context: html, text, full: html, text
• fixup broken zcat for Mac, fix broken FTP options refs #14987 #16763
  
  • src/utils/userApps/fetchChromSizes - lines changed 50, context: html, text, full: html, text
• Added rheMac8; refs #16744
  
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 19, context: html, text, full: html, text
• initial files done, repeat masking done, starting genbank refs #16744
  
  • src/hg/makeDb/doc/rheMac8/initialBuild.txt - lines changed 660, context: html, text, full: html, text
• Added rheMac8; refs #16744
  
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 1, context: html, text, full: html, text
• initial files from makeGenomeDb.pl refs #16744
  
  • src/hg/makeDb/trackDb/rhesus/rheMac8/description.html - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/rheMac8/gap.html - lines changed 32, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/rheMac8/gold.html - lines changed 35, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/rheMac8/trackDb.ra - lines changed 8, context: html, text, full: html, text
• adding rheMac8 refs #16744
  
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
• first pass as display of metadata for NCBI RefSeq track, needs improvement refs #13673
  
  • src/hg/hgc/hgc.c - lines changed 74, context: html, text, full: html, text
  • src/hg/inc/ncbiRefSeqLink.h - lines changed 80, context: html, text, full: html, text
  • src/hg/lib/ncbiRefSeqLink.as - lines changed 22, context: html, text, full: html, text
  • src/hg/lib/ncbiRefSeqLink.c - lines changed 254, context: html, text, full: html, text
  • src/hg/lib/ncbiRefSeqLink.sql - lines changed 28, context: html, text, full: html, text
• labels on ncbiRefSeqBigPsl track refs #13673
  
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 10, context: html, text, full: html, text
• adding ncbiRefSeqLink.c to the build refs #13673
  
  • src/hg/lib/makefile - lines changed 3, context: html, text, full: html, text
• improving formatting of ncbiRefSeq click data refs #13673
  
  • src/hg/hgc/hgc.c - lines changed 146, context: html, text, full: html, text
• remove Brian_s ncbiRefGene definitions refs #13673
  
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 54, context: html, text, full: html, text
• remove Brian_s prNcbiRefGeneInfo business refs #13673
  
  • src/hg/hgc/hgc.c - lines changed 33, context: html, text, full: html, text
• formatting page for ncbiRefSeq refs #13673
  
  • src/hg/hgc/hgc.c - lines changed 49, context: html, text, full: html, text
• trying to get the psl alignment to display refs #13673
  
  • src/hg/hgc/hgc.c - lines changed 18, context: html, text, full: html, text
• trying to get the psl alignment to display refs #13673
  
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 24, context: html, text, full: html, text
• subsume existing UCSC refseq track into ncbi refseq composite refs #13673
  
  • src/hg/makeDb/trackDb/trackDb.genbank.new.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 67, context: html, text, full: html, text
• join the NCBI RefSeq track tables refs #13673
  
  • src/hg/makeDb/schema/all.joiner - lines changed 10, context: html, text, full: html, text
• v328 final build refs #16669
  
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 3, context: html, text, full: html, text
• New version number v328
  
  • src/hg/inc/versionInfo.h - lines changed 1, context: html, text, full: html, text