File Changes for markd

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

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src/hg/geneBounds/clusterGenes/clusterGenes.c
- lines changed 29, 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/tests/expected/ignoreBasesTinyTest.gl
- 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/tests/input/Mt-tRNA.gp
- lines changed 4, 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/tests/makefile
- lines changed 7, 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/hgTracks/hgTracks.c
- lines changed 2, 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/snakeTrack.c
- lines changed 1, context: html, text, full: html, text
  a102654e776e2ba96af731cac5b8cda1803fa3cb Sat Dec 12 22:05:26 2020 -0800
  make it more obvious that HAL screwed up and didn't set error message
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  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
- 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/makeDb/doc/hg19.gencode.txt
- lines changed 48, context: html, text, full: html, text
  f2825cfe9d599d3970bf2379395e912451080d15 Mon Dec 21 23:16:17 2020 -0800
  import of gencdoe V36lift37
src/hg/makeDb/doc/hg38/gencode.txt
- lines changed 35, context: html, text, full: html, text
  8f6ed988e6b529bea3c89bd51a04055956a91327 Sun Dec 20 13:38:03 2020 -0800
  import of all gencode V35
- lines changed 34, context: html, text, full: html, text
  f695b16331ac22d8925e99a05aecd7ce563e0a08 Mon Dec 21 21:29:40 2020 -0800
  import gencodeV36
src/hg/makeDb/outside/gencode/bin/gencodeGenerateTrackDbsOldSchema
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  f695b16331ac22d8925e99a05aecd7ce563e0a08 Mon Dec 21 21:29:40 2020 -0800
  import gencodeV36
src/hg/makeDb/outside/gencode/gencodeLoad.mk
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  8f6ed988e6b529bea3c89bd51a04055956a91327 Sun Dec 20 13:38:03 2020 -0800
  import of all gencode V35
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  f695b16331ac22d8925e99a05aecd7ce563e0a08 Mon Dec 21 21:29:40 2020 -0800
  import gencodeV36
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  f2825cfe9d599d3970bf2379395e912451080d15 Mon Dec 21 23:16:17 2020 -0800
  import of gencdoe V36lift37
src/hg/makeDb/schema/all.joiner
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  f695b16331ac22d8925e99a05aecd7ce563e0a08 Mon Dec 21 21:29:40 2020 -0800
  import gencodeV36
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  f2825cfe9d599d3970bf2379395e912451080d15 Mon Dec 21 23:16:17 2020 -0800
  import of gencdoe V36lift37
src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
- lines changed 1, context: html, text, full: html, text
  f2825cfe9d599d3970bf2379395e912451080d15 Mon Dec 21 23:16:17 2020 -0800
  import of gencdoe V36lift37
src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
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  f2825cfe9d599d3970bf2379395e912451080d15 Mon Dec 21 23:16:17 2020 -0800
  import of gencdoe V36lift37
src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV36lift37.html
- lines changed 32, context: html, text, full: html, text
  f2825cfe9d599d3970bf2379395e912451080d15 Mon Dec 21 23:16:17 2020 -0800
  import of gencdoe V36lift37
src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV36lift37.ra
- lines changed 224, context: html, text, full: html, text
  f2825cfe9d599d3970bf2379395e912451080d15 Mon Dec 21 23:16:17 2020 -0800
  import of gencdoe V36lift37
src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
- lines changed 2, context: html, text, full: html, text
  f695b16331ac22d8925e99a05aecd7ce563e0a08 Mon Dec 21 21:29:40 2020 -0800
  import gencodeV36
src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeSuper.html
- lines changed 4, context: html, text, full: html, text
  f695b16331ac22d8925e99a05aecd7ce563e0a08 Mon Dec 21 21:29:40 2020 -0800
  import gencodeV36
src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV35.html
- lines changed 1, context: html, text, full: html, text
  8f6ed988e6b529bea3c89bd51a04055956a91327 Sun Dec 20 13:38:03 2020 -0800
  import of all gencode V35
src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV36.html
- lines changed 47, context: html, text, full: html, text
  f695b16331ac22d8925e99a05aecd7ce563e0a08 Mon Dec 21 21:29:40 2020 -0800
  import gencodeV36
src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV36.ra
- lines changed 286, context: html, text, full: html, text
  f695b16331ac22d8925e99a05aecd7ce563e0a08 Mon Dec 21 21:29:40 2020 -0800
  import gencodeV36
src/inc/common.mk
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  880d0ccc0f725d16e5b6ed9405bec57d766f0b23 Sun Dec 13 12:23:27 2020 -0800
  updated snake tracks to use latest HAL, which has some perforemance improvements
- lines changed 6, 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

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