File Changes for markd

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
• 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
  • lines changed 17, context: html, text, full: html, text
    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/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/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.
  • lines changed 9, context: html, text, full: html, text
    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/mm39/gencode.txt
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    c616cb4971fb62f396957d38fe123e3b689744d2 Tue May 14 00:34:06 2024 -0700
    import of GENCODE VM35
• 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
  • lines changed 1, context: html, text, full: html, text
    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
  • lines changed 1, context: html, text, full: html, text
    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.
  • lines changed 2, context: html, text, full: html, text
    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
  • lines changed 6, context: html, text, full: html, text
    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
  • lines changed 3, context: html, text, full: html, text
    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
  • lines changed 1, context: html, text, full: html, text
    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
  • lines changed 1, context: html, text, full: html, text
    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
  • lines changed 1995, context: html, text, full: html, text
    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
  • lines changed 74, context: html, text, full: html, text
    f42f0a335bac6371c989f6251acd34a82ce20cec Mon May 13 14:21:11 2024 -0700
    added option to drop certain transcript to support filter lift back problem clases
  • lines changed 74, context: html, text, full: html, text
    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
  • lines changed 89, context: html, text, full: html, text
    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
  • lines changed 1, context: html, text, full: html, text
    c6cc8633fc898187cefc3d3a8969c3381be9fa0f Tue May 14 00:35:32 2024 -0700
    add V46lift37 to trackDb
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
  • lines changed 6, context: html, text, full: html, text
    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
  • lines changed 32, context: html, text, full: html, text
    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
  • lines changed 210, context: html, text, full: html, text
    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/wgEncodeGencodeSuper.html
  • lines changed 4, context: html, text, full: html, text
    8541001ae3a49443eea4234a2f4a32e274dd9b44 Mon May 13 12:00:41 2024 -0700
    import of final release of gencode V46
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV46.html
  • lines changed 1, context: html, text, full: html, text
    8541001ae3a49443eea4234a2f4a32e274dd9b44 Mon May 13 12:00:41 2024 -0700
    import of final release of gencode V46
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV46.ra
  • lines changed 2, context: html, text, full: html, text
    8541001ae3a49443eea4234a2f4a32e274dd9b44 Mon May 13 12:00:41 2024 -0700
    import of final release of gencode V46
• 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
  • lines changed 1, context: html, text, full: html, text
    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/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
• 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
    merge blatHuge implementation
• 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/memalloc.c
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    b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700
    merge blatHuge implementation
• 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
• 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
  • lines changed 144, context: html, text, full: html, text
    c631d4d20178d19ed60da27cd7e34d63872d4a90 Thu May 16 10:34:45 2024 -0700
    added pslSpliceJunctions to gather information in splice junctions to use in comprative mapping analysis
  • lines changed 1, context: html, text, full: html, text
    48cc0aa29826d6f6e99357a12eda728d76a7d132 Fri May 17 02:31:33 2024 -0700
    fixed error in pslSpliceJunctions TSV header
• src/utils/pslSpliceJunctions/tests/expected/rnahg38Test.tsv
  • lines changed 64, context: html, text, full: html, text
    c631d4d20178d19ed60da27cd7e34d63872d4a90 Thu May 16 10:34:45 2024 -0700
    added pslSpliceJunctions to gather information in splice junctions to use in comprative mapping analysis
  • lines changed 1, context: html, text, full: html, text
    48cc0aa29826d6f6e99357a12eda728d76a7d132 Fri May 17 02:31:33 2024 -0700
    fixed error in pslSpliceJunctions TSV header
• src/utils/pslSpliceJunctions/tests/input/rna-hg38.psl
  • lines changed 3, context: html, text, full: html, text
    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
  • lines changed 21, context: html, text, full: html, text
    c631d4d20178d19ed60da27cd7e34d63872d4a90 Thu May 16 10:34:45 2024 -0700
    added pslSpliceJunctions to gather information in splice junctions to use in comprative mapping analysis