Commits for markd

v430_base to v431_preview (2022-04-25 to 2022-05-02) v431

d77f68cb2aedf8aa2a4951671d9fd391b2eab153 Mon Apr 25 22:17:21 2022 -0700

• added SGDP copy number tracks
  • src/hg/makeDb/doc/chm13v2.0userData/build.txt - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0userData/html/sgdpCopyNumber.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0userData/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0userData/trackDb/sedefSegDups.trackDb.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0userData/trackDb/sgdpCopyNumber.trackDb.txt - lines changed 3498, context: html, text, full: html, text

6391bfb6e9dfe4e7a408bb48ce36c85349766c46 Tue Apr 26 18:53:38 2022 -0700

• added CHM13 ENCODE tracks
  • src/hg/makeDb/doc/chm13v2.0userData/build.txt - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0userData/html/encode.html - lines changed 39, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0userData/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0userData/trackDb/encode.trackDb.txt - lines changed 1601, context: html, text, full: html, text

678ed67d021746d2952c1cb85ce47078bea17c72 Tue Apr 26 19:17:48 2022 -0700

• fixed invalid characters in encode doc page
  • src/hg/makeDb/doc/chm13v2.0userData/html/encode.html - lines changed 3, context: html, text, full: html, text

54a8de5f8364d2890ef8d414ac51a507050cc3f6 Thu Apr 28 11:32:49 2022 -0700

• added T2T generated repeat masker tracks
  • src/hg/makeDb/doc/chm13v2.0userData/build.txt - lines changed 60, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0userData/html/t2tRepeatMasker-dense-mode.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/makeDb/doc/chm13v2.0userData/html/t2tRepeatMasker-full-mode.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/makeDb/doc/chm13v2.0userData/html/t2tRepeatMasker-orig-pack-mode.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/makeDb/doc/chm13v2.0userData/html/t2tRepeatMasker-pack-mode.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/makeDb/doc/chm13v2.0userData/html/t2tRepeatMasker.html - lines changed 10911, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0userData/makefile - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0userData/trackDb/sedefSegDups.trackDb.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/chm13v2.0userData/trackDb/t2tRepeatMasker.trackDb.txt - lines changed 10, context: html, text, full: html, text

cb95ab0ac3de81c54babc8b9ba1326d93901ad96 Fri Apr 22 09:27:25 2022 -0700

• import of All GENCODE V40
  • src/hg/makeDb/doc/hg38/gencode.txt - lines changed 42, 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/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

ce16b1fd8bd824c6da07e6f427c389bdbb27ddc6 Sun Apr 24 17:01:44 2022 -0700

• corrected help doc on PSL column names
  • src/utils/chromToUcsc/chromToUcsc - lines changed 1, context: html, text, full: html, text

7df932575ba939fae740a585065f8bc3781851d7 Thu Apr 28 15:28:47 2022 -0700

• import GENCODE mouse VM29
  • src/hg/makeDb/doc/mm39/gencode.txt - lines changed 31, 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/mouse/mm39/wgEncodeGencodeSuper.html - lines changed 4, context: html, text, full: html, text

df27ff9b4c8c6b68d14208aeafb1413f7d3437da Fri Apr 29 09:47:18 2022 -0700

• import V40lift37
  • src/hg/makeDb/doc/hg19.gencode.txt - lines changed 27, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/gencodeLoad.mk - lines changed 2, context: html, text, full: html, text

d821c2aa244dc0d0dd2f7e1d917d9def4026dbe7 Fri Apr 29 10:01:31 2022 -0700

• need to include mm39 and hg19 gencode updates in ra file
  • src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra - lines changed 1, context: html, text, full: html, text