Commits for markd

v299_base to v300_preview (2014-04-28 to 2014-05-05) v300

• added pslMap option to limit mapping alignments to those prefixed with the cooresponding input qName
  • src/hg/utils/pslMap/pslMap.c - lines changed 39, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/expected/testMapFileWithInQName.psl - lines changed 17, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/input/gencode.blocks.qName-psl - lines changed 17, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/input/gencode.src.psl - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/pslMap/tests/makefile - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/pslMap/usage.txt - lines changed 3, context: html, text, full: html, text
• in uniprot database, flag primary gene name to distingiush it from synonyms
  • src/hg/protein/makefile - lines changed 8, context: html, text, full: html, text
  • src/hg/protein/spToDb/expected/test1/gene.txt - lines changed 12, context: html, text, full: html, text
  • src/hg/protein/spToDb/spDb.sql - lines changed 1, context: html, text, full: html, text
  • src/hg/protein/spToDb/spDbTables.as - lines changed 1, context: html, text, full: html, text
  • src/hg/protein/spToDb/spToDb.c - lines changed 3, context: html, text, full: html, text
• run uniprot databases tests as part of standard test run
  • src/hg/makefile - lines changed 1, context: html, text, full: html, text
• remove uncessary noise output from programs
  • src/hg/altSplice/altSplice/genePredToBed.c - lines changed 3, context: html, text, full: html, text
  • src/hg/altSplice/altSplice/genePredToPsl.c - lines changed 3, context: html, text, full: html, text