Commits for braney

v399_preview2 to v399_base (2020-05-25 to 2020-06-01) v399

e4b95e1845f752954f388a0c61b7d4a107baa80a Wed May 27 18:02:07 2020 -0700

• don't count frameshifts as small introns
  • src/hg/lib/variantProjector.c - lines changed 1, context: html, text, full: html, text

a8a289ed81fa32737a91d784a3ebcc1c886770e7 Fri May 29 11:31:31 2020 -0700

• Revert "don't count frameshifts as small introns" This reverts commit e4b95e1845f752954f388a0c61b7d4a107baa80a.
  • src/hg/lib/variantProjector.c - lines changed 1, context: html, text, full: html, text

d93f47cd567bb70aba94de233054e8b4fae00f7d Fri May 29 15:33:58 2020 -0700

• remove frameshifts from psls in hgVai
  • src/hg/lib/annoGratorGpVar.c - lines changed 1, context: html, text, full: html, text
  • src/inc/psl.h - lines changed 3, context: html, text, full: html, text
  • src/lib/psl.c - lines changed 21, context: html, text, full: html, text

7455616a47bc45dbaf93df347345abe1747390c1 Sat May 30 09:10:32 2020 -0700

• add tests for pslRemoveFrameShifts
  • src/utils/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/pslRemoveFrameShifts/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/pslRemoveFrameShifts/pslRemoveFrameShifts.c - lines changed 45, context: html, text, full: html, text
  • src/utils/pslRemoveFrameShifts/tests/expected/negative.psl - lines changed 1, context: html, text, full: html, text
  • src/utils/pslRemoveFrameShifts/tests/expected/positive.psl - lines changed 1, context: html, text, full: html, text
  • src/utils/pslRemoveFrameShifts/tests/input/negative.psl - lines changed 1, context: html, text, full: html, text
  • src/utils/pslRemoveFrameShifts/tests/input/positive.psl - lines changed 1, context: html, text, full: html, text
  • src/utils/pslRemoveFrameShifts/tests/makefile - lines changed 22, context: html, text, full: html, text

3c575ff9551ac6cb939a4ee7f9516d41e0a9c4d0 Mon Jun 1 10:02:00 2020 -0700

• v399 final build
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 3, context: html, text, full: html, text

b07650d95d9277aced9e2027203659b0729a1060 Mon Jun 1 10:03:46 2020 -0700

• New version number v399
  • src/hg/inc/versionInfo.h - lines changed 1, context: html, text, full: html, text
  • src/inc/srcVersion.h - lines changed 1, context: html, text, full: html, text