All File Changes

v465_base to v466_preview (2024-05-13 to 2024-05-20) v466

• .gitignore
  • lines changed 2, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• confs/hgwbeta.hg.conf
  • lines changed 2, context: html, text, full: html, text
    f8ba0e3038e3972c6890eeb001a09d212991c035 Sun May 19 01:11:18 2024 -0700
    Installing updated hg.conf files from UCSC servers
• src/blat/.gitignore
  • lines changed 1, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/hCrea.geno
  • lines changed 100, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/hCrea.mrna
  • lines changed 23, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/hCrea.pep
  • lines changed 7, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/mCrea.geno
  • lines changed 114, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/mCrea.mrna
  • lines changed 24, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/mCrea.pep
  • lines changed 7, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/makefile
  • lines changed 44, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/refFine.psl
  • lines changed 6, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/refProt.psl
  • lines changed 7, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/refProtX.psl
  • lines changed 6, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/refRna.psl
  • lines changed 6, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/refRnaX.psl
  • lines changed 6, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/test/basic/hCrea.geno
  • lines changed 100, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/test/basic/hCrea.mrna
  • lines changed 23, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/test/basic/hCrea.pep
  • lines changed 7, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/test/basic/mCrea.geno
  • lines changed 114, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/test/basic/mCrea.mrna
  • lines changed 24, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/test/basic/mCrea.pep
  • lines changed 7, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/test/basic/refFine.psl
  • lines changed 6, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/test/basic/refProt.psl
  • lines changed 7, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/test/basic/refProtX.psl
  • lines changed 6, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/test/basic/refRna.psl
  • lines changed 6, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/test/basic/refRnaX.psl
  • lines changed 6, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/test/hugeProt/lungfish.prot.psl
  • lines changed 18, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/test/hugeTrans/lungfish.rna.psl
  • lines changed 885, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/test/hugeUntrans/lungfish.rna.psl
  • lines changed 275, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/test/intron50k/expected/test1.psl
  • lines changed 6, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/test/intron50k/expected/test2.psl
  • lines changed 7, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/test/intron50k/expected/test3.psl
  • lines changed 8, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/test/intron50k/test1.psl
  • lines changed 6, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/test/intron50k/test2.psl
  • lines changed 7, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/test/intron50k/test3.psl
  • lines changed 8, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/test/makefile
  • lines changed 70, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/test/throwback/.gitignore
  • lines changed 1, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/test/throwback/test.psl
  • lines changed 8, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/test/v29skips/.gitignore
  • lines changed 1, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/test/v29skips/ex1.psl
  • lines changed 6, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/test/v29skips/ex1_reference.psl
  • lines changed 6, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/test/v29skips/ex2.psl
  • lines changed 6, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/test/v29skips/ex2_reference.psl
  • lines changed 6, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/blat/version.doc
  • lines changed 4, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfClient/AB000095.fa
  • lines changed 49, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfClient/AB000220.fa
  • lines changed 39, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfClient/makefile
  • lines changed 12, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfClient/repeat.fa
  • lines changed 7, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfClient/test1.fa
  • lines changed 11, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfClient/test2.fa
  • lines changed 7, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfClient/test3.fa
  • lines changed 9, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfClient/tests/expected/AB000095.psl
  • lines changed 1, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfClient/tests/expected/AB000220.psl
  • lines changed 1, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfClient/tests/expected/repeat.psl
  • lines changed 89, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfClient/tests/expected/test1.psl
  • lines changed 1, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfClient/tests/expected/test2.psl
  • lines changed 1, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfClient/tests/expected/test3.psl
  • lines changed 74, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfClient/tests/input/AB000095.fa
  • lines changed 49, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfClient/tests/input/AB000220.fa
  • lines changed 39, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfClient/tests/input/repeat.fa
  • lines changed 7, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfClient/tests/input/test1.fa
  • lines changed 11, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfClient/tests/input/test2.fa
  • lines changed 7, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfClient/tests/input/test3.fa
  • lines changed 9, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfClient/tests/makefile
  • lines changed 17, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/.gitignore
  • lines changed 1, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/gfServer.c
  • lines changed 18, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/makefile
  • lines changed 46, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/bin/runHugeTest
  • lines changed 46, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/bin/testDynServer
  • lines changed 22, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/bin/testDynServerPcr
  • lines changed 22, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/bin/testDynServerPerSeqMax
  • lines changed 24, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/bin/testDynServerTrans
  • lines changed 22, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/bin/testDynServerWithDir
  • lines changed 22, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/bin/testIndexFile
  • lines changed 22, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/bin/testIndexFileTrans
  • lines changed 22, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/bin/testPcr
  • lines changed 13, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/bin/testProtNib
  • lines changed 15, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/bin/testProtTwoBit
  • lines changed 15, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/bin/testTransNib
  • lines changed 15, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/bin/testTransTwoBit
  • lines changed 15, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/dynTester
  • lines changed 7, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/expected/directNibTest.out
  • lines changed 24, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/expected/directTwoBitTest.out
  • lines changed 21, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/expected/testHugeProt.out
  • lines changed 60, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/expected/testHugeProt.psl
  • lines changed 11, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/expected/testHugeTrans.out
  • lines changed 2680, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/expected/testHugeTrans.psl
  • lines changed 933, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/expected/testHugeUntrans.out
  • lines changed 102, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/expected/testHugeUntrans.psl
  • lines changed 142, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/expected/testIndexFile
  • lines changed 20, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/expected/testIndexFileTrans
  • lines changed 94, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/expected/testNib.out
  • lines changed 24, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/expected/testTwoBit.out
  • lines changed 21, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/input/lungfish.prot.fa
  • lines changed 47, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/input/lungfish.rna.fa
  • lines changed 206, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/makefile
  • lines changed 113, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/testDynServer
  • lines changed 17, context: html, text, full: html, text
    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/testDynServerPcr
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    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/testDynServerPerSeqMax
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    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/testDynServerTrans
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    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/testDynServerWithDir
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    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/testIndexFile
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    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/testIndexFileTrans
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    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/testPcr
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    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/testProtNib
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    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/testProtTwoBit
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    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/testTransNib
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    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/gfServer/tests/testTransTwoBit
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    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/hg/cgilib/cartTrackDb.c
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    c6ce277e36a537437a04146c8fa7adebb40428ff Wed May 15 12:10:42 2024 -0700
    Libify some searching code so checkHgFindSpec can use it. Make checkHgFindSpec use the same code path as hgSearch so it can correctly test the search correctly, refs #33731
• src/hg/checkHgFindSpec/checkHgFindSpec.c
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    c6ce277e36a537437a04146c8fa7adebb40428ff Wed May 15 12:10:42 2024 -0700
    Libify some searching code so checkHgFindSpec can use it. Make checkHgFindSpec use the same code path as hgSearch so it can correctly test the search correctly, refs #33731
• src/hg/checkHgFindSpec/makefile
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    c6ce277e36a537437a04146c8fa7adebb40428ff Wed May 15 12:10:42 2024 -0700
    Libify some searching code so checkHgFindSpec can use it. Make checkHgFindSpec use the same code path as hgSearch so it can correctly test the search correctly, refs #33731
• src/hg/hgGene/primers.c
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    f1e8687aac05c8b770b4b4ac3184d82fece1bc6c Tue May 14 13:19:34 2024 -0700
    Updating the ExonPrimer URL for the 'Primer design for this transcript' section on hgGene, refs #33080
• src/hg/hgPhyloPlace/phyloPlace.c
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    2d05d30ed4df1612d72ba84c812d004de935b122 Fri May 17 16:08:54 2024 -0700
    Add lib module mmHash (memory-mapped hash), util tabToMmHash, and hgPhyloPlace support for using mmHash files instead of tab-separated files for metadata and name lookup. Using mmHash for name lookup saves about 50-55 seconds for SARS-CoV-2 hgPhyloPlace name/ID queries.
• src/hg/hgPhyloPlace/phyloPlace.h
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    2d05d30ed4df1612d72ba84c812d004de935b122 Fri May 17 16:08:54 2024 -0700
    Add lib module mmHash (memory-mapped hash), util tabToMmHash, and hgPhyloPlace support for using mmHash files instead of tab-separated files for metadata and name lookup. Using mmHash for name lookup saves about 50-55 seconds for SARS-CoV-2 hgPhyloPlace name/ID queries.
• src/hg/hgPhyloPlace/runUsher.c
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    540a3af876ace305fdd16c70ef29b83a1c139f39 Fri May 17 15:37:47 2024 -0700
    minor: make reportTiming messages more explicit about when server is failing over to command line
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
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    2d05d30ed4df1612d72ba84c812d004de935b122 Fri May 17 16:08:54 2024 -0700
    Add lib module mmHash (memory-mapped hash), util tabToMmHash, and hgPhyloPlace support for using mmHash files instead of tab-separated files for metadata and name lookup. Using mmHash for name lookup saves about 50-55 seconds for SARS-CoV-2 hgPhyloPlace name/ID queries.
• src/hg/hgPhyloPlace/vcfFromFasta.c
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    2d05d30ed4df1612d72ba84c812d004de935b122 Fri May 17 16:08:54 2024 -0700
    Add lib module mmHash (memory-mapped hash), util tabToMmHash, and hgPhyloPlace support for using mmHash files instead of tab-separated files for metadata and name lookup. Using mmHash for name lookup saves about 50-55 seconds for SARS-CoV-2 hgPhyloPlace name/ID queries.
• src/hg/hgSearch/hgSearch.c
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    c6ce277e36a537437a04146c8fa7adebb40428ff Wed May 15 12:10:42 2024 -0700
    Libify some searching code so checkHgFindSpec can use it. Make checkHgFindSpec use the same code path as hgSearch so it can correctly test the search correctly, refs #33731
• src/hg/hgTables/hgTables.c
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    c6ce277e36a537437a04146c8fa7adebb40428ff Wed May 15 12:10:42 2024 -0700
    Libify some searching code so checkHgFindSpec can use it. Make checkHgFindSpec use the same code path as hgSearch so it can correctly test the search correctly, refs #33731
• src/hg/hgTracks/exportedDataHubs.c
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    877d275fba2154784c6dd114641ad9ba7881a860 Thu May 16 10:18:51 2024 -0700
    Close div when printing exported data hubs, refs #33700
• src/hg/hgTracks/hgTracks.c
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    c6ce277e36a537437a04146c8fa7adebb40428ff Wed May 15 12:10:42 2024 -0700
    Libify some searching code so checkHgFindSpec can use it. Make checkHgFindSpec use the same code path as hgSearch so it can correctly test the search correctly, refs #33731
• src/hg/hgTracks/menu.c
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    bfbc825c0932c9444ba781517f9cf4034aac233b Mon May 13 14:43:00 2024 -0700
    Change hgTracks view dna link to not have the hgsid twice, refs #33691
• src/hg/hgVai/hgVai.c
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    c6ce277e36a537437a04146c8fa7adebb40428ff Wed May 15 12:10:42 2024 -0700
    Libify some searching code so checkHgFindSpec can use it. Make checkHgFindSpec use the same code path as hgSearch so it can correctly test the search correctly, refs #33731
• src/hg/htdocs/FAQ/FAQdownloads.html
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    39b458cbf20d613b1acc53c085d2416423379fe1 Thu May 16 16:28:32 2024 -0700
    Creating a JASPAR FAQ for users who are trying to view only one transcription factor or download the data using the Table Browser, refs #33581
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    e27a06b381eff1b24a133e9cb7ee64bee936750e Thu May 16 16:41:44 2024 -0700
    Adding a line break, refs #33581
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    f6226d5305e218d853a909fc92ccbaed181666b4 Thu May 16 17:02:04 2024 -0700
    Fixing a typo Gerardo noticed, refs #33581
• src/hg/htdocs/contacts.html
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    8f7879fda04070339f87a73602ad5dde349034c8 Wed May 15 13:49:05 2024 -0700
    Feedback from CR refs #33566
• src/hg/htdocs/goldenPath/help/customTrackText.html
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    bbe7c3ee9e306ef4cf003321c8c420f1c68f5d3e Tue May 14 14:11:38 2024 -0700
    Reformatting the 'creating a session' steps, refs #19736
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    c6582ecb0ccf13141e44395c11adec3d32d2ac9a Tue May 14 17:24:46 2024 -0700
    Adding links to the hosting documentation on the custom track help page, refs #23633
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    764d83af431c94bae59ae2bbd7e25b86ab693cb4 Tue May 14 17:31:55 2024 -0700
    Adding the word 'NOTE:' to make the section stand out more, refs #23633
• src/hg/htdocs/goldenPath/newsarch.html
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    72ba20be6279aca3555b1b3703b5570adf5dd0ed Tue May 14 02:57:19 2024 -0700
    improving bot trap, as the display none didnt work
• src/hg/htdocs/images/jasparSetting.png
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    0d2b620e6024ee262db68d7b3f99ef3bfcc396da Thu May 16 15:43:27 2024 -0700
    Adding two screenshots for a JASPAR FAQ, refs #33581
• src/hg/htdocs/images/jasparTB.png
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    0d2b620e6024ee262db68d7b3f99ef3bfcc396da Thu May 16 15:43:27 2024 -0700
    Adding two screenshots for a JASPAR FAQ, refs #33581
• src/hg/htdocs/robots.rr.txt
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    2db7ef26b75fcc5078a116edb2681ea88d578708 Tue May 14 03:04:53 2024 -0700
    adding more AI bots to robots.rr.txt, email thread with browser-staff
• src/hg/hubApi/search.c
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    c6ce277e36a537437a04146c8fa7adebb40428ff Wed May 15 12:10:42 2024 -0700
    Libify some searching code so checkHgFindSpec can use it. Make checkHgFindSpec use the same code path as hgSearch so it can correctly test the search correctly, refs #33731
• src/hg/inc/cartTrackDb.h
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    c6ce277e36a537437a04146c8fa7adebb40428ff Wed May 15 12:10:42 2024 -0700
    Libify some searching code so checkHgFindSpec can use it. Make checkHgFindSpec use the same code path as hgSearch so it can correctly test the search correctly, refs #33731
• src/hg/inc/hgFind.h
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    c6ce277e36a537437a04146c8fa7adebb40428ff Wed May 15 12:10:42 2024 -0700
    Libify some searching code so checkHgFindSpec can use it. Make checkHgFindSpec use the same code path as hgSearch so it can correctly test the search correctly, refs #33731
• src/hg/js/hgGateway.js
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    e2ed08acdca884ab4bceaaab4a7386437a846634 Tue May 14 12:12:18 2024 -0700
    Fix native assemblies not being selectable in hgGateway autocomplete, refs #33572
• src/hg/js/utils.js
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    747cedcf600f86c8d981ab597c94b89e178b9ed6 Thu May 16 10:19:28 2024 -0700
    Remove click & drag to scroll tooltip from hgTracks image, refs #33700
• src/hg/lib/cart.c
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    9f499752613f1e37b2984a354ffb577df68f274e Tue May 14 10:40:49 2024 -0700
    deal with '0' as database due to some magic I wrote 20 years ago
• src/hg/lib/hgFind.c
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    c6ce277e36a537437a04146c8fa7adebb40428ff Wed May 15 12:10:42 2024 -0700
    Libify some searching code so checkHgFindSpec can use it. Make checkHgFindSpec use the same code path as hgSearch so it can correctly test the search correctly, refs #33731
• src/hg/lib/hui.c
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    25367be1ea1cf374e19f3773f276cc6a0faa651d Thu May 16 10:43:16 2024 -0700
    change "Reset filters" label to "Clear filters", as that is really what the button does RM 33727
• src/hg/lib/straw/new_straw.cpp
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    1f7ca2af6629a710ba3888ea8f684ec19203a625 Mon May 20 09:40:58 2024 -0700
    Initial unmodified commit of most recent straw library files
• src/hg/lib/straw/new_straw.h
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    1f7ca2af6629a710ba3888ea8f684ec19203a625 Mon May 20 09:40:58 2024 -0700
    Initial unmodified commit of most recent straw library files
• src/hg/makeDb/dbDbToHubTxt/dbDbToHubTxt.c
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    8cf5d084511a9bbd9d28edf8f5508d9df1ff98eb Mon May 13 14:41:26 2024 -0700
    in the absence of a 2bit file assume it is a track hub attach to a GenArk hub
• src/hg/makeDb/doc/bigDbSnp.txt
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    91814318ba5e9eec945f690b2598e390f407c7a0 Fri May 17 17:24:12 2024 -0700
    Update dbSnp153 to fix comma-formatting problem as Galt did for dbSnp155. refs #33070
• src/hg/makeDb/doc/hg19.gencode.txt
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    70fde199fda0e697d5c0e5e01470ff433fa00dc1 Tue May 14 00:06:40 2024 -0700
    Import of GENCODE V46lift37, including add an option to import code to drop specific transcripts. This deals incorrectly included PAR transcript.
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    f4aa15bef8c781b695f09979a28a9beb68c90963 Wed May 15 00:09:39 2024 -0700
    change workaround for gencode gene symbol file with short rows
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    3f6eb7eb31edcf73fc79707baeda85cf70e52992 Wed May 15 08:12:10 2024 -0700
    re-import fixed version of GENCODE V46lift37 gene symbol table from EBI
• src/hg/makeDb/doc/hg38/gencode.txt
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    8541001ae3a49443eea4234a2f4a32e274dd9b44 Mon May 13 12:00:41 2024 -0700
    import of final release of gencode V46
• src/hg/makeDb/doc/hg38/gnomad.txt
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    dde908e5381a6da2e78aea5c8ae38c6dcff2cd46 Tue Feb 6 09:46:42 2024 -0800
    Staging gnomAD v4, including reorganizing tracks so v4.1 bigBed are first after the v4 VCF, description pages changes and makedoc, refs #33746
• src/hg/makeDb/doc/mm39/gencode.txt
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    c616cb4971fb62f396957d38fe123e3b689744d2 Tue May 14 00:34:06 2024 -0700
    import of GENCODE VM35
• src/hg/makeDb/doc/pairBrowse/hg38-JAHBBZ010000038.1.txt
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    e0fa53bc686c9aed8e712e76638a00933e3a560f Sun May 19 16:48:21 2024 -0700
    ongoing work on pair browser
• src/hg/makeDb/doc/pairBrowse/hg38-JAHEOV010000036.1.txt
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    e0fa53bc686c9aed8e712e76638a00933e3a560f Sun May 19 16:48:21 2024 -0700
    ongoing work on pair browser
• src/hg/makeDb/outside/gencode/bin/buildGencodeToUcscLift
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    f42f0a335bac6371c989f6251acd34a82ce20cec Mon May 13 14:21:11 2024 -0700
    added option to drop certain transcript to support filter lift back problem clases
• src/hg/makeDb/outside/gencode/bin/gencodeBackMapMetadataIds
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    f42f0a335bac6371c989f6251acd34a82ce20cec Mon May 13 14:21:11 2024 -0700
    added option to drop certain transcript to support filter lift back problem clases
• src/hg/makeDb/outside/gencode/bin/gencodeExonSupportToTable
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    f42f0a335bac6371c989f6251acd34a82ce20cec Mon May 13 14:21:11 2024 -0700
    added option to drop certain transcript to support filter lift back problem clases
• src/hg/makeDb/outside/gencode/bin/gencodeGxfToAttrs
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    f42f0a335bac6371c989f6251acd34a82ce20cec Mon May 13 14:21:11 2024 -0700
    added option to drop certain transcript to support filter lift back problem clases
• src/hg/makeDb/outside/gencode/bin/gencodeGxfToGenePred
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    f42f0a335bac6371c989f6251acd34a82ce20cec Mon May 13 14:21:11 2024 -0700
    added option to drop certain transcript to support filter lift back problem clases
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    70fde199fda0e697d5c0e5e01470ff433fa00dc1 Tue May 14 00:06:40 2024 -0700
    Import of GENCODE V46lift37, including add an option to import code to drop specific transcripts. This deals incorrectly included PAR transcript.
• src/hg/makeDb/outside/gencode/bin/gencodeMakeAttrs
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    f42f0a335bac6371c989f6251acd34a82ce20cec Mon May 13 14:21:11 2024 -0700
    added option to drop certain transcript to support filter lift back problem clases
• src/hg/makeDb/outside/gencode/bin/gencodeMakeTracks
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    f42f0a335bac6371c989f6251acd34a82ce20cec Mon May 13 14:21:11 2024 -0700
    added option to drop certain transcript to support filter lift back problem clases
• src/hg/makeDb/outside/gencode/bin/gencodePolyaGxfToGenePred
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    f42f0a335bac6371c989f6251acd34a82ce20cec Mon May 13 14:21:11 2024 -0700
    added option to drop certain transcript to support filter lift back problem clases
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
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    8541001ae3a49443eea4234a2f4a32e274dd9b44 Mon May 13 12:00:41 2024 -0700
    import of final release of gencode V46
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    70fde199fda0e697d5c0e5e01470ff433fa00dc1 Tue May 14 00:06:40 2024 -0700
    Import of GENCODE V46lift37, including add an option to import code to drop specific transcripts. This deals incorrectly included PAR transcript.
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    132eda4ef5ec2d89a572ab1732672a345a5a1cef Tue May 14 00:33:51 2024 -0700
    import of GENCODE VM35
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    f4aa15bef8c781b695f09979a28a9beb68c90963 Wed May 15 00:09:39 2024 -0700
    change workaround for gencode gene symbol file with short rows
• src/hg/makeDb/outside/gencode/lib/gencode/__init__.py
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    f42f0a335bac6371c989f6251acd34a82ce20cec Mon May 13 14:21:11 2024 -0700
    added option to drop certain transcript to support filter lift back problem clases
• src/hg/makeDb/outside/gencode/lib/gencode/gencodeGenes.py
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    f42f0a335bac6371c989f6251acd34a82ce20cec Mon May 13 14:21:11 2024 -0700
    added option to drop certain transcript to support filter lift back problem clases
• src/hg/makeDb/outside/gencode/lib/gencode/gencodeProcess.py
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    f42f0a335bac6371c989f6251acd34a82ce20cec Mon May 13 14:21:11 2024 -0700
    added option to drop certain transcript to support filter lift back problem clases
• src/hg/makeDb/outside/gencode/lib/gencode/gencodeTags.py
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    f42f0a335bac6371c989f6251acd34a82ce20cec Mon May 13 14:21:11 2024 -0700
    added option to drop certain transcript to support filter lift back problem clases
• src/hg/makeDb/outside/gencode/tests/expected/buildGencodeToUcscLiftHs38Test.chain
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    5f18ea51c37c998166e6ec19d62fde6537323d75 Mon May 13 14:09:04 2024 -0700
    updated test results due to chain changes
• src/hg/makeDb/outside/gencode/tests/expected/specialCases1Test.gp
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    f42f0a335bac6371c989f6251acd34a82ce20cec Mon May 13 14:21:11 2024 -0700
    added option to drop certain transcript to support filter lift back problem clases
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    62c5cbd5c584c147c2d11904a4b23d666ff07f95 Tue May 14 01:27:38 2024 -0700
    update gencode expected results due to order difference merge on MT mappings
• src/hg/makeDb/schema/all.joiner
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    70fde199fda0e697d5c0e5e01470ff433fa00dc1 Tue May 14 00:06:40 2024 -0700
    Import of GENCODE V46lift37, including add an option to import code to drop specific transcripts. This deals incorrectly included PAR transcript.
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
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    c6cc8633fc898187cefc3d3a8969c3381be9fa0f Tue May 14 00:35:32 2024 -0700
    add V46lift37 to trackDb
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
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    70fde199fda0e697d5c0e5e01470ff433fa00dc1 Tue May 14 00:06:40 2024 -0700
    Import of GENCODE V46lift37, including add an option to import code to drop specific transcripts. This deals incorrectly included PAR transcript.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV46lift37.html
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    70fde199fda0e697d5c0e5e01470ff433fa00dc1 Tue May 14 00:06:40 2024 -0700
    Import of GENCODE V46lift37, including add an option to import code to drop specific transcripts. This deals incorrectly included PAR transcript.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV46lift37.ra
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    70fde199fda0e697d5c0e5e01470ff433fa00dc1 Tue May 14 00:06:40 2024 -0700
    Import of GENCODE V46lift37, including add an option to import code to drop specific transcripts. This deals incorrectly included PAR transcript.
• src/hg/makeDb/trackDb/human/hg38/gnomad.alpha.ra
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    dde908e5381a6da2e78aea5c8ae38c6dcff2cd46 Tue Feb 6 09:46:42 2024 -0800
    Staging gnomAD v4, including reorganizing tracks so v4.1 bigBed are first after the v4 VCF, description pages changes and makedoc, refs #33746
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    00d05b703b0cb8fccd9dc7b6685db685a90fff1e Thu May 16 15:45:58 2024 -0700
    Remove old gnomAD PLI track from gnomad alpha ra file, refs #33746
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
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    dde908e5381a6da2e78aea5c8ae38c6dcff2cd46 Tue Feb 6 09:46:42 2024 -0800
    Staging gnomAD v4, including reorganizing tracks so v4.1 bigBed are first after the v4 VCF, description pages changes and makedoc, refs #33746
• src/hg/makeDb/trackDb/human/hg38/gnomadV4.1.html
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    dde908e5381a6da2e78aea5c8ae38c6dcff2cd46 Tue Feb 6 09:46:42 2024 -0800
    Staging gnomAD v4, including reorganizing tracks so v4.1 bigBed are first after the v4 VCF, description pages changes and makedoc, refs #33746
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    dde908e5381a6da2e78aea5c8ae38c6dcff2cd46 Tue Feb 6 09:46:42 2024 -0800
    Staging gnomAD v4, including reorganizing tracks so v4.1 bigBed are first after the v4 VCF, description pages changes and makedoc, refs #33746
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    75a9210ce048b8638d0b3a618c4ccf270fc8c58c Sun May 19 22:20:21 2024 -0700
    Staging the GENCODE v46/vM35 KnownGene tracks on hgwbeta, refs #33080 #33083
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeSuper.html
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    8541001ae3a49443eea4234a2f4a32e274dd9b44 Mon May 13 12:00:41 2024 -0700
    import of final release of gencode V46
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV46.html
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    8541001ae3a49443eea4234a2f4a32e274dd9b44 Mon May 13 12:00:41 2024 -0700
    import of final release of gencode V46
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV46.ra
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    8541001ae3a49443eea4234a2f4a32e274dd9b44 Mon May 13 12:00:41 2024 -0700
    import of final release of gencode V46
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
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    75a9210ce048b8638d0b3a618c4ccf270fc8c58c Sun May 19 22:20:21 2024 -0700
    Staging the GENCODE v46/vM35 KnownGene tracks on hgwbeta, refs #33080 #33083
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeSuper.html
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    132eda4ef5ec2d89a572ab1732672a345a5a1cef Tue May 14 00:33:51 2024 -0700
    import of GENCODE VM35
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM35.html
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    132eda4ef5ec2d89a572ab1732672a345a5a1cef Tue May 14 00:33:51 2024 -0700
    import of GENCODE VM35
• src/hg/mouseStuff/regionPicker/regionPicker.c
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    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/hg/utils/buildPairAssembly/buildPairAssembly.c
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    7e49f8f7b02b41d0bab2051250a3a08ce4ffafd0 Fri May 17 11:45:39 2024 -0700
    ongoing work on pairBrowser
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    e0fa53bc686c9aed8e712e76638a00933e3a560f Sun May 19 16:48:21 2024 -0700
    ongoing work on pair browser
• src/hg/utils/buildPairAssembly/makePair
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    7e49f8f7b02b41d0bab2051250a3a08ce4ffafd0 Fri May 17 11:45:39 2024 -0700
    ongoing work on pairBrowser
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    e0fa53bc686c9aed8e712e76638a00933e3a560f Sun May 19 16:48:21 2024 -0700
    ongoing work on pair browser
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
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    07d759a94ed39950bd7634e0f3e0cc717d7a7b3c Tue May 14 16:26:03 2024 -0700
    Remove unused annotation option from datasets download command; split into larger chunks when rerunning pangolin on all sequences.
• src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv
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    871f3a2b4ce77de9ef002db5098411d25022cb75 Tue May 14 16:24:27 2024 -0700
    Fixed 21F (Iota) path, added 24A (JN.1) and 24B (JN.1.11.1).
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
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    b6e717ddc3b002501765ad91dd087253669311ee Wed May 15 15:49:21 2024 -0700
    Added latest newly designated lineages.
• src/inc/bits.h
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    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/inc/common.h
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    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
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    2d05d30ed4df1612d72ba84c812d004de935b122 Fri May 17 16:08:54 2024 -0700
    Add lib module mmHash (memory-mapped hash), util tabToMmHash, and hgPhyloPlace support for using mmHash files instead of tab-separated files for metadata and name lookup. Using mmHash for name lookup saves about 50-55 seconds for SARS-CoV-2 hgPhyloPlace name/ID queries.
• src/inc/genoFind.h
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    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/inc/gfPcrLib.h
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    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
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• src/inc/mmHash.h
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    2d05d30ed4df1612d72ba84c812d004de935b122 Fri May 17 16:08:54 2024 -0700
    Add lib module mmHash (memory-mapped hash), util tabToMmHash, and hgPhyloPlace support for using mmHash files instead of tab-separated files for metadata and name lookup. Using mmHash for name lookup saves about 50-55 seconds for SARS-CoV-2 hgPhyloPlace name/ID queries.
• src/inc/userApp.mk
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    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/jkOwnLib/genoFind.c
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    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/jkOwnLib/makefile
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    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/jkOwnLib/patSpace.c
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    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/lib/bits.c
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    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• src/lib/common.c
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    2d05d30ed4df1612d72ba84c812d004de935b122 Fri May 17 16:08:54 2024 -0700
    Add lib module mmHash (memory-mapped hash), util tabToMmHash, and hgPhyloPlace support for using mmHash files instead of tab-separated files for metadata and name lookup. Using mmHash for name lookup saves about 50-55 seconds for SARS-CoV-2 hgPhyloPlace name/ID queries.
• src/lib/makefile
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    2d05d30ed4df1612d72ba84c812d004de935b122 Fri May 17 16:08:54 2024 -0700
    Add lib module mmHash (memory-mapped hash), util tabToMmHash, and hgPhyloPlace support for using mmHash files instead of tab-separated files for metadata and name lookup. Using mmHash for name lookup saves about 50-55 seconds for SARS-CoV-2 hgPhyloPlace name/ID queries.
• src/lib/memalloc.c
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    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
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• src/lib/mmHash.c
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    2d05d30ed4df1612d72ba84c812d004de935b122 Fri May 17 16:08:54 2024 -0700
    Add lib module mmHash (memory-mapped hash), util tabToMmHash, and hgPhyloPlace support for using mmHash files instead of tab-separated files for metadata and name lookup. Using mmHash for name lookup saves about 50-55 seconds for SARS-CoV-2 hgPhyloPlace name/ID queries.
• src/lib/tests/expected/mmHashTest.mmh
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    2d05d30ed4df1612d72ba84c812d004de935b122 Fri May 17 16:08:54 2024 -0700
    Add lib module mmHash (memory-mapped hash), util tabToMmHash, and hgPhyloPlace support for using mmHash files instead of tab-separated files for metadata and name lookup. Using mmHash for name lookup saves about 50-55 seconds for SARS-CoV-2 hgPhyloPlace name/ID queries.
• src/lib/tests/expected/mmHashTest.out
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    2d05d30ed4df1612d72ba84c812d004de935b122 Fri May 17 16:08:54 2024 -0700
    Add lib module mmHash (memory-mapped hash), util tabToMmHash, and hgPhyloPlace support for using mmHash files instead of tab-separated files for metadata and name lookup. Using mmHash for name lookup saves about 50-55 seconds for SARS-CoV-2 hgPhyloPlace name/ID queries.
• src/lib/tests/input/mmHashTest.txt
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    2d05d30ed4df1612d72ba84c812d004de935b122 Fri May 17 16:08:54 2024 -0700
    Add lib module mmHash (memory-mapped hash), util tabToMmHash, and hgPhyloPlace support for using mmHash files instead of tab-separated files for metadata and name lookup. Using mmHash for name lookup saves about 50-55 seconds for SARS-CoV-2 hgPhyloPlace name/ID queries.
• src/lib/tests/makefile
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    2d05d30ed4df1612d72ba84c812d004de935b122 Fri May 17 16:08:54 2024 -0700
    Add lib module mmHash (memory-mapped hash), util tabToMmHash, and hgPhyloPlace support for using mmHash files instead of tab-separated files for metadata and name lookup. Using mmHash for name lookup saves about 50-55 seconds for SARS-CoV-2 hgPhyloPlace name/ID queries.
• src/lib/tests/mmHashTest.c
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    2d05d30ed4df1612d72ba84c812d004de935b122 Fri May 17 16:08:54 2024 -0700
    Add lib module mmHash (memory-mapped hash), util tabToMmHash, and hgPhyloPlace support for using mmHash files instead of tab-separated files for metadata and name lookup. Using mmHash for name lookup saves about 50-55 seconds for SARS-CoV-2 hgPhyloPlace name/ID queries.
• src/utils/makefile
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    c631d4d20178d19ed60da27cd7e34d63872d4a90 Thu May 16 10:34:45 2024 -0700
    added pslSpliceJunctions to gather information in splice junctions to use in comprative mapping analysis
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    ad7ff98d8aeec25df511d5f764ce1b6697321c7c Fri May 17 16:33:34 2024 -0700
    Added new util tabToMmHash to UCSC_APPS so it's in top-level build but not userApps.
• src/utils/pslSpliceJunctions/makefile
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    c631d4d20178d19ed60da27cd7e34d63872d4a90 Thu May 16 10:34:45 2024 -0700
    added pslSpliceJunctions to gather information in splice junctions to use in comprative mapping analysis
• src/utils/pslSpliceJunctions/pslSpliceJunctions.c
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    c631d4d20178d19ed60da27cd7e34d63872d4a90 Thu May 16 10:34:45 2024 -0700
    added pslSpliceJunctions to gather information in splice junctions to use in comprative mapping analysis
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    48cc0aa29826d6f6e99357a12eda728d76a7d132 Fri May 17 02:31:33 2024 -0700
    fixed error in pslSpliceJunctions TSV header
• src/utils/pslSpliceJunctions/tests/expected/rnahg38Test.tsv
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    c631d4d20178d19ed60da27cd7e34d63872d4a90 Thu May 16 10:34:45 2024 -0700
    added pslSpliceJunctions to gather information in splice junctions to use in comprative mapping analysis
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    48cc0aa29826d6f6e99357a12eda728d76a7d132 Fri May 17 02:31:33 2024 -0700
    fixed error in pslSpliceJunctions TSV header
• src/utils/pslSpliceJunctions/tests/input/rna-hg38.psl
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    c631d4d20178d19ed60da27cd7e34d63872d4a90 Thu May 16 10:34:45 2024 -0700
    added pslSpliceJunctions to gather information in splice junctions to use in comprative mapping analysis
• src/utils/pslSpliceJunctions/tests/makefile
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    c631d4d20178d19ed60da27cd7e34d63872d4a90 Thu May 16 10:34:45 2024 -0700
    added pslSpliceJunctions to gather information in splice junctions to use in comprative mapping analysis
• src/utils/qa/weeklybld/buildEnv.csh
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    a4faf4b2c09241c808b8ee32271a701e841d7b62 Mon May 20 10:08:11 2024 -0700
    v466 preview1, refs #33577
• src/utils/tabToMmHash/makefile
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    2d05d30ed4df1612d72ba84c812d004de935b122 Fri May 17 16:08:54 2024 -0700
    Add lib module mmHash (memory-mapped hash), util tabToMmHash, and hgPhyloPlace support for using mmHash files instead of tab-separated files for metadata and name lookup. Using mmHash for name lookup saves about 50-55 seconds for SARS-CoV-2 hgPhyloPlace name/ID queries.
• src/utils/tabToMmHash/tabToMmHash.c
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    2d05d30ed4df1612d72ba84c812d004de935b122 Fri May 17 16:08:54 2024 -0700
    Add lib module mmHash (memory-mapped hash), util tabToMmHash, and hgPhyloPlace support for using mmHash files instead of tab-separated files for metadata and name lookup. Using mmHash for name lookup saves about 50-55 seconds for SARS-CoV-2 hgPhyloPlace name/ID queries.

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