Commits for markd

v425_preview to v425_preview2 (2021-12-13 to 2021-12-20) v425

312002c4b4015a4e5acedd47dad9e5d6b8d3c1b1 Mon Nov 22 18:38:59 2021 -0800

• move rmskAlign and rmskJoined to lib so it they can be used by programs
  • src/hg/cgilib/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/cgilib/rmskAlign.c - lines changed 212, context: html, text, full: html, text
  • src/hg/cgilib/rmskJoined.c - lines changed 215, context: html, text, full: html, text
  • src/hg/lib/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/rmskAlign.c - lines changed 212, context: html, text, full: html, text
  • src/hg/lib/rmskJoined.c - lines changed 215, context: html, text, full: html, text

54805fea0022a5d8d26ce1eadc2ac470a0b564ef Fri Dec 17 18:53:31 2021 -0800

• Pass through PSLs without modification when -repsAsMatch is used. This allows for doing repeat cotent analysis even filtering.
  • src/hg/pslCDnaFilter/cDnaAligns.c - lines changed 23, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/cDnaAligns.h - lines changed 4, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/cDnaReader.c - lines changed 8, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/pslCDnaFilter.c - lines changed 3, context: html, text, full: html, text
  • src/hg/pslCDnaFilter/tests/expected/repsAsMatchTest/keep.psl - lines changed 8, context: html, text, full: html, text