File Changes for hiram

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v446_base to v447_preview (2023-04-03 to 2023-04-10) v447

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src/hg/hubApi/apiUtils.c
- lines changed 24, context: html, text, full: html, text
  9cc4ce16befd7694963bdb46b6e9b4d28a6930cc Thu Apr 6 14:29:04 2023 -0700
  adding endpoint /list/files function to list hgdownload files refs #23589
- lines changed 17, context: html, text, full: html, text
  57ad409a6278ef6a75e2c082988ed1ee419a5f78 Fri Apr 7 11:35:09 2023 -0700
  now allowing argument format=text on list files output refs #23589
- lines changed 16, context: html, text, full: html, text
  763252113893b5fa89e1b08a8a306e396770592a Fri Apr 7 12:47:11 2023 -0700
  correct header output for plain text and add comment lines as per standard JSON output, TODO: manage error outputs refs #23589
src/hg/hubApi/dataApi.h
- lines changed 14, context: html, text, full: html, text
  9cc4ce16befd7694963bdb46b6e9b4d28a6930cc Thu Apr 6 14:29:04 2023 -0700
  adding endpoint /list/files function to list hgdownload files refs #23589
- lines changed 7, context: html, text, full: html, text
  57ad409a6278ef6a75e2c082988ed1ee419a5f78 Fri Apr 7 11:35:09 2023 -0700
  now allowing argument format=text on list files output refs #23589
src/hg/hubApi/hubApi.c
- lines changed 5, context: html, text, full: html, text
  9cc4ce16befd7694963bdb46b6e9b4d28a6930cc Thu Apr 6 14:29:04 2023 -0700
  adding endpoint /list/files function to list hgdownload files refs #23589
- lines changed 1, context: html, text, full: html, text
  57ad409a6278ef6a75e2c082988ed1ee419a5f78 Fri Apr 7 11:35:09 2023 -0700
  now allowing argument format=text on list files output refs #23589
src/hg/hubApi/list.c
- lines changed 111, context: html, text, full: html, text
  9cc4ce16befd7694963bdb46b6e9b4d28a6930cc Thu Apr 6 14:29:04 2023 -0700
  adding endpoint /list/files function to list hgdownload files refs #23589
- lines changed 97, context: html, text, full: html, text
  57ad409a6278ef6a75e2c082988ed1ee419a5f78 Fri Apr 7 11:35:09 2023 -0700
  now allowing argument format=text on list files output refs #23589
- lines changed 1, context: html, text, full: html, text
  763252113893b5fa89e1b08a8a306e396770592a Fri Apr 7 12:47:11 2023 -0700
  correct header output for plain text and add comment lines as per standard JSON output, TODO: manage error outputs refs #23589
src/hg/hubApi/tests/expected/err07.gz
- lines changed 0, context: html, text, full: html, text
  9cc4ce16befd7694963bdb46b6e9b4d28a6930cc Thu Apr 6 14:29:04 2023 -0700
  adding endpoint /list/files function to list hgdownload files refs #23589
src/hg/hubApi/tests/expected/err09.gz
- lines changed 0, context: html, text, full: html, text
  9cc4ce16befd7694963bdb46b6e9b4d28a6930cc Thu Apr 6 14:29:04 2023 -0700
  adding endpoint /list/files function to list hgdownload files refs #23589
src/hg/hubApi/tests/expected/err10.gz
- lines changed 0, context: html, text, full: html, text
  9cc4ce16befd7694963bdb46b6e9b4d28a6930cc Thu Apr 6 14:29:04 2023 -0700
  adding endpoint /list/files function to list hgdownload files refs #23589
src/hg/hubApi/tests/expected/list03.gz
- lines changed 0, context: html, text, full: html, text
  eabb83a3bb858d06c2329802c9ad4131a908e78b Thu Apr 6 14:35:59 2023 -0700
  ce11 now has hg38 chain track refs #23589
src/hg/hubApi/tests/expected/list09.gz
- lines changed 0, context: html, text, full: html, text
  eabb83a3bb858d06c2329802c9ad4131a908e78b Thu Apr 6 14:35:59 2023 -0700
  ce11 now has hg38 chain track refs #23589
src/hg/hubApi/tests/expected/list22.gz
- lines changed 0, context: html, text, full: html, text
  2df046ea76491116b288c27a6fc91d6b3e84f7ee Thu Apr 6 14:48:44 2023 -0700
  adding tests for /list/files function db and GenArk genome refs #23589
- lines changed 0, context: html, text, full: html, text
  39aeb562a83a5d024984c793a7338e33083b498f Fri Apr 7 12:56:37 2023 -0700
  adding tests for /list/files with maxItemsOutput and format=text options refs #23589
src/hg/hubApi/tests/expected/list23.gz
- lines changed 0, context: html, text, full: html, text
  2df046ea76491116b288c27a6fc91d6b3e84f7ee Thu Apr 6 14:48:44 2023 -0700
  adding tests for /list/files function db and GenArk genome refs #23589
- lines changed 0, context: html, text, full: html, text
  39aeb562a83a5d024984c793a7338e33083b498f Fri Apr 7 12:56:37 2023 -0700
  adding tests for /list/files with maxItemsOutput and format=text options refs #23589
src/hg/hubApi/tests/expected/list24.gz
- lines changed 0, context: html, text, full: html, text
  39aeb562a83a5d024984c793a7338e33083b498f Fri Apr 7 12:56:37 2023 -0700
  adding tests for /list/files with maxItemsOutput and format=text options refs #23589
src/hg/hubApi/tests/expected/list25.gz
- lines changed 0, context: html, text, full: html, text
  39aeb562a83a5d024984c793a7338e33083b498f Fri Apr 7 12:56:37 2023 -0700
  adding tests for /list/files with maxItemsOutput and format=text options refs #23589
src/hg/hubApi/tests/makefile
- lines changed 2, context: html, text, full: html, text
  9cc4ce16befd7694963bdb46b6e9b4d28a6930cc Thu Apr 6 14:29:04 2023 -0700
  adding endpoint /list/files function to list hgdownload files refs #23589
- lines changed 13, context: html, text, full: html, text
  2df046ea76491116b288c27a6fc91d6b3e84f7ee Thu Apr 6 14:48:44 2023 -0700
  adding tests for /list/files function db and GenArk genome refs #23589
- lines changed 14, context: html, text, full: html, text
  39aeb562a83a5d024984c793a7338e33083b498f Fri Apr 7 12:56:37 2023 -0700
  adding tests for /list/files with maxItemsOutput and format=text options refs #23589
src/hg/makeDb/doc/asmHubs/master.run.list
- lines changed 24, context: html, text, full: html, text
  6495d1c198950df4012b38356c734716f034f4ca Wed Apr 5 13:47:03 2023 -0700
  finished up HPRC and continuing CCGP refs #30508
- lines changed 15, context: html, text, full: html, text
  2a4aa562c332332ac0bb21bdc10f564d7022bbf5 Fri Apr 7 13:31:40 2023 -0700
  continue adding CCGP genome browsers refs #30912
src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
- lines changed 8, context: html, text, full: html, text
  7af99fba157b9b57be6317a713a2064f8a242740 Wed Apr 5 15:19:17 2023 -0700
  adding 7 CCGP assemblies refs #30912
- lines changed 3, context: html, text, full: html, text
  42f85d1985de90df0b8d6888dad0edd0ab6f315d Fri Apr 7 13:59:01 2023 -0700
  adding three for CCGP refs #30912
src/hg/makeDb/doc/ccgpAsmHub/ccgp.orderList.tsv
- lines changed 25, context: html, text, full: html, text
  67acf4489044ecb0ae388000d82ed54f12f5c207 Fri Apr 7 14:26:10 2023 -0700
  catching up completed CCGP assemblies refs #30912
src/hg/makeDb/doc/ccgpAsmHub/ccgp.taxId.asmId.class.txt
- lines changed 2, context: html, text, full: html, text
  bb32c5cb690a1aed9ad0660b89c8ca2260a3bbcc Fri Apr 7 14:35:16 2023 -0700
  catching up two missed before refs #30912
src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
- lines changed 1, context: html, text, full: html, text
  fd66a1ec1128f13b9e2ca96c151ff6b7fafc40db Wed Apr 5 15:26:54 2023 -0700
  adding one from CCGP refs #30912
- lines changed 3, context: html, text, full: html, text
  fce661f760040f46c9a7b9dcad35b1f56bb633dd Fri Apr 7 14:10:15 2023 -0700
  adding 3 for CCGP refs #30912
src/hg/makeDb/doc/hg38/hprcLastz.txt
- lines changed 1098, context: html, text, full: html, text
  0842d5714831ed96499cb0e5c69a2f5f78a1de13 Tue Apr 4 09:55:15 2023 -0700
  continue lastz runs for HPRC genomes to hg38 refs #30508
- lines changed 1012, context: html, text, full: html, text
  0d6e74b5c4f8a5c5aa4465d6fb5551dec1fc3841 Wed Apr 5 16:27:34 2023 -0700
  catching up with completed lastz/chain/net refs #30912
- lines changed 92, context: html, text, full: html, text
  ca5e96d3ef0bc2d2f995a912dc4f7b5fdf432e4e Wed Apr 5 16:46:20 2023 -0700
  catching up with completed lastz/chain/net refs #30912
- lines changed 1104, context: html, text, full: html, text
  5ed537d9f4f1883a4596f278c9c13cb7816df964 Thu Apr 6 15:07:58 2023 -0700
  catching up with completed lastz/chain/net refs #30912
- lines changed 34, context: html, text, full: html, text
  9a9b4e595e833b4f0f52875567b7e68c7f2270b8 Thu Apr 6 15:10:55 2023 -0700
  catching up with completed lastz/chain/net refs #30912
- lines changed 92, context: html, text, full: html, text
  722f05d417cfe7733d360889b901f4d54c4a38dc Thu Apr 6 15:23:14 2023 -0700
  eliminate a duplicate entry refs #30912
- lines changed 4508, context: html, text, full: html, text
  e263797cef1d906754ad02475540f35528b92e63 Mon Apr 10 07:45:39 2023 -0700
  almost done HPRC lastz runs refs #30912
- lines changed 184, context: html, text, full: html, text
  0a532517e84e7897ed50f2ea333134daaa1387c0 Mon Apr 10 07:49:48 2023 -0700
  one HPRC lastz run outstanding refs #30912
- lines changed 92, context: html, text, full: html, text
  b390872e7b2543685b9bd8e301099c38935bcc1d Mon Apr 10 08:12:30 2023 -0700
  last one has completed refs #30912
src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
- lines changed 9, context: html, text, full: html, text
  eda51609835cc537c7284e5ec44b7ae08e343e7d Fri Apr 7 14:08:55 2023 -0700
  catching up CCGP assemblies refs #30912
src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
- lines changed 2, context: html, text, full: html, text
  3f75f2912bd5dcfdcfa4e4ef4f27e17970bb76a0 Wed Apr 5 16:47:57 2023 -0700
  adding one for CCGP refs #30912
src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
- lines changed 2, context: html, text, full: html, text
  8e449f42069370b1d0c0884e943c1ad7f1aa2cde Wed Apr 5 15:44:58 2023 -0700
  adding 2 from CCGP refs #30912
- lines changed 1, context: html, text, full: html, text
  fbf619e3e0dc16ece1838ebdc8b613e49edbccb7 Fri Apr 7 13:45:51 2023 -0700
  adding one for the CCGP project refs #30912
src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
- lines changed 3, context: html, text, full: html, text
  5b270f8510130fbd83cea83cb4a4e3b9937c2bca Wed Apr 5 15:45:46 2023 -0700
  adding 3 from CCGP refs #30912
- lines changed 4, context: html, text, full: html, text
  5e55032b06e858e91b7baf8441d80d3007356655 Fri Apr 7 14:02:15 2023 -0700
  adding 4 for CCGP refs #30912
src/hg/utils/automation/asmHubTrackDb.sh
- lines changed 30, context: html, text, full: html, text
  80ef5aceda1a2e29e3e1e654c8de191848405cda Fri Apr 7 10:23:32 2023 -0700
  tolerate ebiGene for HPRC project refs #30508
src/hg/utils/automation/pairLastz.sh
- lines changed 43, context: html, text, full: html, text
  2332b3a609d7fc057db833551347b1be5f2555b4 Fri Apr 7 10:19:16 2023 -0700
  show total run time and construct trackDb when possible in the GenArk hub no redmine

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