Commits for larrym

v261_base to v262_preview (2012-01-03 to 2012-01-10) v262

• use cloneString to fix a "using freed memory" problem (see redmine 6467)
  • src/hg/lib/fileUi.c - lines changed 1, context: html, text, full: html, text
• add bamChromList
  • src/inc/bamFile.h - lines changed 12, context: html, text, full: html, text
  • src/lib/bamFile.c - lines changed 76, context: html, text, full: html, text
• support -host, -user and -password
  • src/hg/utils/makeTableList/makeTableList.c - lines changed 15, context: html, text, full: html, text
• suppress too verbose messages in samtools >= 0.1.18; see redmine #6491
  • src/lib/bamFile.c - lines changed 7, context: html, text, full: html, text
• add synonym for stop-loss, which appears in snp135 data (see redmine #6419)
  • src/hg/lib/snp125Ui.c - lines changed 1, context: html, text, full: html, text
• check for illegal chromosomes in bam and big* track loaders (redmine #2572)
  • src/hg/lib/customFactory.c - lines changed 49, context: html, text, full: html, text