Commits for markd

v408_base to v409_preview (2020-12-07 to 2021-01-04) v409

a102654e776e2ba96af731cac5b8cda1803fa3cb Sat Dec 12 22:05:26 2020 -0800

• make it more obvious that HAL screwed up and didn't set error message
  • src/hg/hgTracks/snakeTrack.c - lines changed 1, context: html, text, full: html, text

9c9af0a5de97e512c5ab9b9b8dd5928499c3f78c Sat Dec 12 22:06:07 2020 -0800

• fixed debug print of CGI URL and arguments
  • src/hg/hgTracks/hgTracks.c - lines changed 2, context: html, text, full: html, text

13a74772a9f4e38f7d13746542de8733a998c07f Sun Dec 13 11:07:22 2020 -0800

• don't add next/prev item to snakes, they are not implemented and crash in a confusing way in code for database tracks
  • src/hg/hgTracks/snakeTrack.c - lines changed 1, context: html, text, full: html, text

61308020150706a0ce4437616eea098620f92f6d Sun Dec 13 11:31:03 2020 -0800

• fixed snake track requesting a negative length of DNA in self-alignments #25987
  • src/hg/hgTracks/snakeTrack.c - lines changed 1, context: html, text, full: html, text

880d0ccc0f725d16e5b6ed9405bec57d766f0b23 Sun Dec 13 12:23:27 2020 -0800

• updated snake tracks to use latest HAL, which has some perforemance improvements
  • src/inc/common.mk - lines changed 5, context: html, text, full: html, text

83657216000f3e3ae3673d8a2a7d04feaf8cd147 Tue Dec 15 13:21:22 2020 -0800

• fixed bug were clusterGenes -ignoreBases would drop small transcripts
  • src/hg/geneBounds/clusterGenes/clusterGenes.c - lines changed 29, context: html, text, full: html, text
  • src/hg/geneBounds/clusterGenes/tests/expected/ignoreBasesTinyTest.gl - lines changed 5, context: html, text, full: html, text
  • src/hg/geneBounds/clusterGenes/tests/input/Mt-tRNA.gp - lines changed 4, context: html, text, full: html, text
  • src/hg/geneBounds/clusterGenes/tests/makefile - lines changed 7, context: html, text, full: html, text

01a64f9d63b8d29bee782ced4e5ce16260089649 Fri Dec 18 15:37:24 2020 -0800

• fix hgTracks bring in uncommon shared library with HAL/HDF5, make CGIs less portable
  • src/inc/common.mk - lines changed 6, context: html, text, full: html, text

8f6ed988e6b529bea3c89bd51a04055956a91327 Sun Dec 20 13:38:03 2020 -0800

• import of all gencode V35
  • src/hg/makeDb/doc/hg38/gencode.txt - lines changed 35, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/gencodeLoad.mk - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV35.html - lines changed 1, context: html, text, full: html, text

f695b16331ac22d8925e99a05aecd7ce563e0a08 Mon Dec 21 21:29:40 2020 -0800

• import gencodeV36
  • src/hg/makeDb/doc/hg38/gencode.txt - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/gencodeGenerateTrackDbsOldSchema - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/gencodeLoad.mk - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/schema/all.joiner - lines changed 94, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeSuper.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV36.html - lines changed 47, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV36.ra - lines changed 286, context: html, text, full: html, text

f2825cfe9d599d3970bf2379395e912451080d15 Mon Dec 21 23:16:17 2020 -0800

• import of gencdoe V36lift37
  • src/hg/makeDb/doc/hg19.gencode.txt - lines changed 48, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/gencodeLoad.mk - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/schema/all.joiner - lines changed 91, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV36lift37.html - lines changed 32, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV36lift37.ra - lines changed 224, context: html, text, full: html, text