File Changes for markd

v498_base to v499_preview (2026-05-11 to 2026-05-18) v499

• .gitignore
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    9b1d1612efa7f321c5d3c500ce799c804c977135 Tue May 12 14:23:51 2026 -0700
    Add to .gitignore update LICENSE to remove htslib just note old htslib directory, not require removal
• .gitmodules
  • lines changed 3, context: html, text, full: html, text
    cc2c8b0181212e97d22db24fc67394f4c634656e Fri Apr 24 20:19:55 2026 -0700
    added htslib submodule
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    2ee9d8c7beac3731a5e835e14921ac4e4cae4f81 Sat Apr 25 11:24:01 2026 -0700
    Moved htslib to submodules/htslib. Removed use of local static shared libraries for libcurl, as UCSC copy is outdated. Add a script that is run to check for htslib submodules being initialized and do the initialization. It also checks for stale src/htslib files
• LICENSE
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    9b1d1612efa7f321c5d3c500ce799c804c977135 Tue May 12 14:23:51 2026 -0700
    Add to .gitignore update LICENSE to remove htslib just note old htslib directory, not require removal
• src/hg/encode3/validateFiles/validateFiles.c
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    3a1b00734b0c19737b48b171decfeb6b9edd27aa Wed May 6 18:16:34 2026 -0700
    Fix issue with new htslib and access to tabix VCF header. Permanently enable tests that would have found this problem. They were disable by a non-extent USE_TABIX make vaiable.
• src/hg/hgTables/bam.c
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    1ff2e18ba5e50dd2d1becd3cd6a25343578c10b8 Tue Apr 21 14:09:04 2026 -0700
    rework of htslib/UDC integration to use htslib hfile driver mechanism
• src/hg/hgTracks/bamTrack.c
  • lines changed 5, context: html, text, full: html, text
    1ff2e18ba5e50dd2d1becd3cd6a25343578c10b8 Tue Apr 21 14:09:04 2026 -0700
    rework of htslib/UDC integration to use htslib hfile driver mechanism
• src/hg/utils/gtfToGenePred/gtfToGenePred.c
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    1fc1fed014272d6781d8f98845efae537e808e58 Sat May 16 20:07:30 2026 -0700
    added option to get attribute output from gtfToGenePred in TSV format
• src/hg/utils/gtfToGenePred/tests/expected/impliedStop.info
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    1fc1fed014272d6781d8f98845efae537e808e58 Sat May 16 20:07:30 2026 -0700
    added option to get attribute output from gtfToGenePred in TSV format
• src/hg/utils/gtfToGenePred/tests/makefile
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    1fc1fed014272d6781d8f98845efae537e808e58 Sat May 16 20:07:30 2026 -0700
    added option to get attribute output from gtfToGenePred in TSV format
• src/htslib
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    cc2c8b0181212e97d22db24fc67394f4c634656e Fri Apr 24 20:19:55 2026 -0700
    added htslib submodule
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    012294051c7f9ded1f8392899feebbebd26ead5c Fri Apr 24 22:03:38 2026 -0700
    makefile will initialize htslib submodule if needed
• src/htslib/INSTALL
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/LICENSE
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/Makefile
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/NEWS
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/README
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/bgzf.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/bgzip.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/config.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/config.h.in
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/config.log
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/config.mk
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/config.mk.in
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/config.status
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/configure
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/configure.ac
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/cram.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/cram_codecs.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/cram_codecs.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/cram_decode.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/cram_decode.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/cram_encode.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/cram_encode.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/cram_external.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/cram_index.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/cram_index.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/cram_io.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/cram_io.c.00
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/cram_io.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/cram_samtools.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/cram_samtools.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/cram_stats.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/cram_stats.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/cram_structs.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/files.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/mFILE.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/mFILE.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/misc.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/open_trace_file.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/open_trace_file.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/os.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/pooled_alloc.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/pooled_alloc.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/rANS_byte.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/rANS_static.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/rANS_static.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/sam_header.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/sam_header.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/string_alloc.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/string_alloc.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/cram/thread_pool.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/thread_pool.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/vlen.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/vlen.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/zfio.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/cram/zfio.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/faidx.5
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/faidx.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/hfile.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/hfile_internal.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/hfile_irods.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
    move copy of htslib
• src/htslib/hfile_libcurl.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/hfile_net.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/hts.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/hts_internal.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/htsfile.1
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/htsfile.c
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/htslib.mk
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/htslib.pc.in
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/htslib/bgzf.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/htslib/cram.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/htslib/faidx.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/htslib/hfile.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/htslib/hts.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/htslib/hts_defs.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/htslib/kbitset.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/htslib/kfunc.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/htslib/khash.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/htslib/khash_str2int.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/htslib/klist.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/htslib/knetfile.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/htslib/kseq.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/htslib/ksort.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/htslib/kstring.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/htslib/regidx.h
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    7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
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• src/htslib/htslib/sam.h
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• src/htslib/htslib/tbx.h
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• src/htslib/test/test-regidx.c
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• src/htslib/test/test-vcf-api.c
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• src/htslib/test/test_view.c
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• src/htslib/test/xx#blank.sam
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• src/htslib/vcf.c
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• src/htslib/vcf_sweep.c
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• src/htslib/vcfutils.c
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• src/inc/bamFile.h
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    1ff2e18ba5e50dd2d1becd3cd6a25343578c10b8 Tue Apr 21 14:09:04 2026 -0700
    rework of htslib/UDC integration to use htslib hfile driver mechanism
• src/inc/common.mk
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    1ff2e18ba5e50dd2d1becd3cd6a25343578c10b8 Tue Apr 21 14:09:04 2026 -0700
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    2ee9d8c7beac3731a5e835e14921ac4e4cae4f81 Sat Apr 25 11:24:01 2026 -0700
    Moved htslib to submodules/htslib. Removed use of local static shared libraries for libcurl, as UCSC copy is outdated. Add a script that is run to check for htslib submodules being initialized and do the initialization. It also checks for stale src/htslib files
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    683ed1ec1118d21c351579f323fa0f5760c91100 Mon May 18 05:32:11 2026 -0700
    add --llzma for non-hgwdev builds
• src/inc/hfileUdc.h
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    1ff2e18ba5e50dd2d1becd3cd6a25343578c10b8 Tue Apr 21 14:09:04 2026 -0700
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• src/inc/udc.h
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    1ff2e18ba5e50dd2d1becd3cd6a25343578c10b8 Tue Apr 21 14:09:04 2026 -0700
    rework of htslib/UDC integration to use htslib hfile driver mechanism
• src/lib/bamFile.c
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    1ff2e18ba5e50dd2d1becd3cd6a25343578c10b8 Tue Apr 21 14:09:04 2026 -0700
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    fe875492a7da5c0f64cd9c6d43cd6809478ec2a4 Sat May 9 08:32:48 2026 -0700
    *.bai and *.tbi index files were by-passing UDC and being downloaded to current directory
• src/lib/hfileUdc.c
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    1ff2e18ba5e50dd2d1becd3cd6a25343578c10b8 Tue Apr 21 14:09:04 2026 -0700
    rework of htslib/UDC integration to use htslib hfile driver mechanism
• src/lib/knetUdc.c
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    1ff2e18ba5e50dd2d1becd3cd6a25343578c10b8 Tue Apr 21 14:09:04 2026 -0700
    rework of htslib/UDC integration to use htslib hfile driver mechanism
• src/lib/linefile.c
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    fe875492a7da5c0f64cd9c6d43cd6809478ec2a4 Sat May 9 08:32:48 2026 -0700
    *.bai and *.tbi index files were by-passing UDC and being downloaded to current directory
• src/lib/makefile
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    1ff2e18ba5e50dd2d1becd3cd6a25343578c10b8 Tue Apr 21 14:09:04 2026 -0700
    rework of htslib/UDC integration to use htslib hfile driver mechanism
• src/lib/tests/expected/vcfHeader1kGNoGenotypes.out
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    3a1b00734b0c19737b48b171decfeb6b9edd27aa Wed May 6 18:16:34 2026 -0700
    Fix issue with new htslib and access to tabix VCF header. Permanently enable tests that would have found this problem. They were disable by a non-extent USE_TABIX make vaiable.
• src/lib/tests/expected/vcfHeader1kGWithGenotypes.out
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    3a1b00734b0c19737b48b171decfeb6b9edd27aa Wed May 6 18:16:34 2026 -0700
    Fix issue with new htslib and access to tabix VCF header. Permanently enable tests that would have found this problem. They were disable by a non-extent USE_TABIX make vaiable.
• src/lib/tests/expected/vcfHeaderOldV3.out
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    3a1b00734b0c19737b48b171decfeb6b9edd27aa Wed May 6 18:16:34 2026 -0700
    Fix issue with new htslib and access to tabix VCF header. Permanently enable tests that would have found this problem. They were disable by a non-extent USE_TABIX make vaiable.
• src/lib/tests/makefile
  • lines changed 25, context: html, text, full: html, text
    3a1b00734b0c19737b48b171decfeb6b9edd27aa Wed May 6 18:16:34 2026 -0700
    Fix issue with new htslib and access to tabix VCF header. Permanently enable tests that would have found this problem. They were disable by a non-extent USE_TABIX make vaiable.
  • lines changed 1, context: html, text, full: html, text
    c113b6a136531a9793170068d067c49f18df77cd Sat May 9 07:32:42 2026 -0700
    Update htslib to handle initialize order issue. Fix test program build order dependency
• src/lib/tests/tabixFetch.c
  • lines changed 2, context: html, text, full: html, text
    3a1b00734b0c19737b48b171decfeb6b9edd27aa Wed May 6 18:16:34 2026 -0700
    Fix issue with new htslib and access to tabix VCF header. Permanently enable tests that would have found this problem. They were disable by a non-extent USE_TABIX make vaiable.
• src/lib/tests/vcfParseTest.c
  • lines changed 30, context: html, text, full: html, text
    3a1b00734b0c19737b48b171decfeb6b9edd27aa Wed May 6 18:16:34 2026 -0700
    Fix issue with new htslib and access to tabix VCF header. Permanently enable tests that would have found this problem. They were disable by a non-extent USE_TABIX make vaiable.
• src/lib/udc.c
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    1ff2e18ba5e50dd2d1becd3cd6a25343578c10b8 Tue Apr 21 14:09:04 2026 -0700
    rework of htslib/UDC integration to use htslib hfile driver mechanism
• src/lib/vcf.c
  • lines changed 34, context: html, text, full: html, text
    3a1b00734b0c19737b48b171decfeb6b9edd27aa Wed May 6 18:16:34 2026 -0700
    Fix issue with new htslib and access to tabix VCF header. Permanently enable tests that would have found this problem. They were disable by a non-extent USE_TABIX make vaiable.
  • lines changed 2, context: html, text, full: html, text
    fe875492a7da5c0f64cd9c6d43cd6809478ec2a4 Sat May 9 08:32:48 2026 -0700
    *.bai and *.tbi index files were by-passing UDC and being downloaded to current directory
• src/makefile
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    012294051c7f9ded1f8392899feebbebd26ead5c Fri Apr 24 22:03:38 2026 -0700
    makefile will initialize htslib submodule if needed
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    2ee9d8c7beac3731a5e835e14921ac4e4cae4f81 Sat Apr 25 11:24:01 2026 -0700
    Moved htslib to submodules/htslib. Removed use of local static shared libraries for libcurl, as UCSC copy is outdated. Add a script that is run to check for htslib submodules being initialized and do the initialization. It also checks for stale src/htslib files
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    22c3e40ac360c345ab79f6bd3a51dbde33b2b4cd Tue May 12 14:25:49 2026 -0700
    move submoduleSet to submodule dir
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    5049589b9025e6961a2aab60f629159033141dc2 Tue May 12 14:31:21 2026 -0700
    run topChecks before any topLibs, even if done in parallel
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    2655a0cce4d565ac1c1c54fcf238b49cba2c5d37 Tue May 12 14:50:08 2026 -0700
    try to make sure topCheck runs first
• src/submoduleSetup
  • lines changed 22, context: html, text, full: html, text
    2ee9d8c7beac3731a5e835e14921ac4e4cae4f81 Sat Apr 25 11:24:01 2026 -0700
    Moved htslib to submodules/htslib. Removed use of local static shared libraries for libcurl, as UCSC copy is outdated. Add a script that is run to check for htslib submodules being initialized and do the initialization. It also checks for stale src/htslib files
  • lines changed 5, context: html, text, full: html, text
    9b1d1612efa7f321c5d3c500ce799c804c977135 Tue May 12 14:23:51 2026 -0700
    Add to .gitignore update LICENSE to remove htslib just note old htslib directory, not require removal
• src/submodules/README.md
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    625a5f2525117ff4c3e5a73ad73c020af9bdd1f5 Wed Apr 29 19:45:37 2026 -0700
    added README for submodules, currently just htslib
• src/submodules/htslib
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    2ee9d8c7beac3731a5e835e14921ac4e4cae4f81 Sat Apr 25 11:24:01 2026 -0700
    Moved htslib to submodules/htslib. Removed use of local static shared libraries for libcurl, as UCSC copy is outdated. Add a script that is run to check for htslib submodules being initialized and do the initialization. It also checks for stale src/htslib files
  • lines changed 1, context: html, text, full: html, text
    c113b6a136531a9793170068d067c49f18df77cd Sat May 9 07:32:42 2026 -0700
    Update htslib to handle initialize order issue. Fix test program build order dependency
• src/submodules/submoduleSetup
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    22c3e40ac360c345ab79f6bd3a51dbde33b2b4cd Tue May 12 14:25:49 2026 -0700
    move submoduleSet to submodule dir
• src/userApps/fetchKentSource.sh
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    1fd0ab8b59002435f0da06a8c5f1525db09024dc Thu Apr 30 20:52:15 2026 -0700
    inital conversion of fetchKentSource, can not test until on github