Commits for markd
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v498_base to v499_preview (2026-05-11 to 2026-05-18) v499
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7df6e18265341f87a69fba808aa1f92f8ebca841 Wed Apr 15 13:39:42 2026 -0700
- move copy of htslib
- src/htslib/config.h.in - lines changed 27, context: html, text, full: html, text
- src/htslib/config.log - lines changed 418, context: html, text, full: html, text
- src/htslib/config.mk.in - lines changed 111, context: html, text, full: html, text
- src/htslib/config.status - lines changed 1003, context: html, text, full: html, text
- src/htslib/configure - lines changed 5267, context: html, text, full: html, text
- src/htslib/configure.ac - lines changed 192, context: html, text, full: html, text
- src/htslib/cram/cram.h - lines changed 61, context: html, text, full: html, text
- src/htslib/cram/cram_codecs.c - lines changed 1949, context: html, text, full: html, text
- src/htslib/cram/cram_codecs.h - lines changed 194, context: html, text, full: html, text
- src/htslib/cram/cram_decode.c - lines changed 3143, context: html, text, full: html, text
- src/htslib/cram/cram_decode.h - lines changed 112, context: html, text, full: html, text
- src/htslib/cram/cram_encode.c - lines changed 3094, context: html, text, full: html, text
- src/htslib/cram/cram_encode.h - lines changed 105, context: html, text, full: html, text
- src/htslib/cram/cram_external.c - lines changed 377, context: html, text, full: html, text
- src/htslib/cram/cram_index.c - lines changed 583, context: html, text, full: html, text
- src/htslib/cram/cram_index.h - lines changed 99, context: html, text, full: html, text
- src/htslib/cram/cram_io.c - lines changed 4599, context: html, text, full: html, text
- src/htslib/cram/cram_io.c.00 - lines changed 4611, context: html, text, full: html, text
- src/htslib/cram/cram_io.h - lines changed 669, context: html, text, full: html, text
- src/htslib/cram/cram_samtools.c - lines changed 149, context: html, text, full: html, text
- src/htslib/cram/cram_samtools.h - lines changed 105, context: html, text, full: html, text
- src/htslib/cram/cram_stats.c - lines changed 448, context: html, text, full: html, text
- src/htslib/cram/cram_stats.h - lines changed 59, context: html, text, full: html, text
- src/htslib/cram/cram_structs.h - lines changed 819, context: html, text, full: html, text
- src/htslib/cram/files.c - lines changed 74, context: html, text, full: html, text
- src/htslib/cram/mFILE.c - lines changed 694, context: html, text, full: html, text
- src/htslib/cram/mFILE.h - lines changed 89, context: html, text, full: html, text
- src/htslib/cram/misc.h - lines changed 110, context: html, text, full: html, text
- src/htslib/cram/open_trace_file.c - lines changed 414, context: html, text, full: html, text
- src/htslib/cram/open_trace_file.h - lines changed 125, context: html, text, full: html, text
- src/htslib/cram/pooled_alloc.c - lines changed 188, context: html, text, full: html, text
- src/htslib/cram/pooled_alloc.h - lines changed 64, context: html, text, full: html, text
- src/htslib/cram/rANS_byte.h - lines changed 336, context: html, text, full: html, text
- src/htslib/cram/rANS_static.c - lines changed 868, context: html, text, full: html, text
- src/htslib/cram/rANS_static.h - lines changed 51, context: html, text, full: html, text
- src/htslib/cram/sam_header.c - lines changed 1268, context: html, text, full: html, text
- src/htslib/cram/sam_header.h - lines changed 459, context: html, text, full: html, text
- src/htslib/cram/string_alloc.c - lines changed 155, context: html, text, full: html, text
- src/htslib/cram/string_alloc.h - lines changed 68, context: html, text, full: html, text
- src/htslib/cram/thread_pool.c - lines changed 813, context: html, text, full: html, text
- src/htslib/cram/thread_pool.h - lines changed 218, context: html, text, full: html, text
- src/htslib/cram/vlen.c - lines changed 430, context: html, text, full: html, text
- src/htslib/cram/vlen.h - lines changed 48, context: html, text, full: html, text
- src/htslib/cram/zfio.c - lines changed 183, context: html, text, full: html, text
- src/htslib/cram/zfio.h - lines changed 62, context: html, text, full: html, text
- src/htslib/hfile_internal.h - lines changed 139, context: html, text, full: html, text
- src/htslib/hfile_irods.c - lines changed 259, context: html, text, full: html, text
- src/htslib/hfile_libcurl.c - lines changed 919, context: html, text, full: html, text
- src/htslib/hfile_net.c - lines changed 114, context: html, text, full: html, text
- src/htslib/hts_internal.h - lines changed 69, context: html, text, full: html, text
- src/htslib/htslib.pc.in - lines changed 10, context: html, text, full: html, text
- src/htslib/htslib/bgzf.h - lines changed 329, context: html, text, full: html, text
- src/htslib/htslib/cram.h - lines changed 492, context: html, text, full: html, text
- src/htslib/htslib/faidx.h - lines changed 137, context: html, text, full: html, text
- src/htslib/htslib/hfile.h - lines changed 215, context: html, text, full: html, text
- src/htslib/htslib/hts.h - lines changed 642, context: html, text, full: html, text
- src/htslib/htslib/hts_defs.h - lines changed 72, context: html, text, full: html, text
- src/htslib/htslib/kbitset.h - lines changed 160, context: html, text, full: html, text
- src/htslib/htslib/kfunc.h - lines changed 83, context: html, text, full: html, text
- src/htslib/htslib/khash.h - lines changed 627, context: html, text, full: html, text
- src/htslib/htslib/khash_str2int.h - lines changed 133, context: html, text, full: html, text
- src/htslib/htslib/klist.h - lines changed 135, context: html, text, full: html, text
- src/htslib/htslib/knetfile.h - lines changed 114, context: html, text, full: html, text
- src/htslib/htslib/kseq.h - lines changed 253, context: html, text, full: html, text
- src/htslib/htslib/ksort.h - lines changed 285, context: html, text, full: html, text
- src/htslib/htslib/kstring.h - lines changed 277, context: html, text, full: html, text
- src/htslib/htslib/regidx.h - lines changed 154, context: html, text, full: html, text
- src/htslib/htslib/sam.h - lines changed 454, context: html, text, full: html, text
- src/htslib/htslib/synced_bcf_reader.h - lines changed 302, context: html, text, full: html, text
- src/htslib/htslib/tbx.h - lines changed 79, context: html, text, full: html, text
- src/htslib/htslib/vcf.h - lines changed 907, context: html, text, full: html, text
- src/htslib/htslib/vcf_sweep.h - lines changed 47, context: html, text, full: html, text
- src/htslib/htslib/vcfutils.h - lines changed 134, context: html, text, full: html, text
- src/htslib/htslib_vars.mk - lines changed 49, context: html, text, full: html, text
- src/htslib/knetfile.c - lines changed 684, context: html, text, full: html, text
- src/htslib/synced_bcf_reader.c - lines changed 1284, context: html, text, full: html, text
- src/htslib/test/auxf#values.sam - lines changed 5, context: html, text, full: html, text
- src/htslib/test/auxf.fa - lines changed 2, context: html, text, full: html, text
- src/htslib/test/auxf.fa.fai - lines changed 1, context: html, text, full: html, text
- src/htslib/test/c1#bounds.sam - lines changed 4, context: html, text, full: html, text
- src/htslib/test/c1#clip.sam - lines changed 8, context: html, text, full: html, text
- src/htslib/test/c1#noseq.sam - lines changed 10, context: html, text, full: html, text
- src/htslib/test/c1#pad1.sam - lines changed 10, context: html, text, full: html, text
- src/htslib/test/c1#pad2.sam - lines changed 14, context: html, text, full: html, text
- src/htslib/test/c1#pad3.sam - lines changed 14, context: html, text, full: html, text
- src/htslib/test/c1#unknown.sam - lines changed 9, context: html, text, full: html, text
- src/htslib/test/c1.fa.fai - lines changed 1, context: html, text, full: html, text
- src/htslib/test/c2#pad.sam - lines changed 26, context: html, text, full: html, text
- src/htslib/test/c2.fa.fai - lines changed 1, context: html, text, full: html, text
- src/htslib/test/ce#1.sam - lines changed 2, context: html, text, full: html, text
- src/htslib/test/ce#2.sam - lines changed 3, context: html, text, full: html, text
- src/htslib/test/ce#5.sam - lines changed 11, context: html, text, full: html, text
- src/htslib/test/ce#5b.sam - lines changed 12, context: html, text, full: html, text
- src/htslib/test/ce#supp.sam - lines changed 6, context: html, text, full: html, text
- src/htslib/test/ce#tag_depadded.sam - lines changed 11, context: html, text, full: html, text
- src/htslib/test/ce#tag_padded.sam - lines changed 11, context: html, text, full: html, text
- src/htslib/test/ce#unmap.sam - lines changed 6, context: html, text, full: html, text
- src/htslib/test/ce#unmap1.sam - lines changed 20, context: html, text, full: html, text
- src/htslib/test/ce#unmap2.sam - lines changed 29, context: html, text, full: html, text
- src/htslib/test/ce.fa - lines changed 20803, context: html, text, full: html, text
- src/htslib/test/ce.fa.fai - lines changed 7, context: html, text, full: html, text
- src/htslib/test/compare_sam.pl - lines changed 194, context: html, text, full: html, text
- src/htslib/test/cross_validate.sh - lines changed 126, context: html, text, full: html, text
- src/htslib/test/faidx.fa - lines changed 17, context: html, text, full: html, text
- src/htslib/test/fieldarith.c - lines changed 72, context: html, text, full: html, text
- src/htslib/test/fieldarith.sam - lines changed 15, context: html, text, full: html, text
- src/htslib/test/hfile.c - lines changed 204, context: html, text, full: html, text
- src/htslib/test/sam.c - lines changed 208, context: html, text, full: html, text
- src/htslib/test/test-regidx.c - lines changed 116, context: html, text, full: html, text
- src/htslib/test/test-vcf-api.c - lines changed 282, context: html, text, full: html, text
- src/htslib/test/test-vcf-api.out - lines changed 28, context: html, text, full: html, text
- src/htslib/test/test-vcf-hdr-in.vcf - lines changed 25, context: html, text, full: html, text
- src/htslib/test/test-vcf-hdr.out - lines changed 16, context: html, text, full: html, text
- src/htslib/test/test-vcf-sweep.c - lines changed 112, context: html, text, full: html, text
- src/htslib/test/test-vcf-sweep.out - lines changed 4, context: html, text, full: html, text
- src/htslib/test/test.pl - lines changed 227, context: html, text, full: html, text
- src/htslib/test/test_view.c - lines changed 194, context: html, text, full: html, text
- src/htslib/test/test_view.pl - lines changed 93, context: html, text, full: html, text
- src/htslib/test/xx#blank.sam - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/htslib/test/xx#large_aux.sam - lines changed 4, context: html, text, full: html, text
- src/htslib/test/xx#large_aux2.sam - lines changed 11, context: html, text, full: html, text
- src/htslib/test/xx#minimal.sam - lines changed 10, context: html, text, full: html, text
- src/htslib/test/xx#pair.sam - lines changed 7, context: html, text, full: html, text
- src/htslib/test/xx#rg.sam - lines changed 13, context: html, text, full: html, text
- src/htslib/test/xx#tlen.sam - lines changed 34, context: html, text, full: html, text
- src/htslib/test/xx#tlen2.sam - lines changed 36, context: html, text, full: html, text
- src/htslib/test/xx#triplet.sam - lines changed 7, context: html, text, full: html, text
- src/htslib/test/xx#unsorted.sam - lines changed 8, context: html, text, full: html, text
- src/htslib/test/xx.fa.fai - lines changed 2, context: html, text, full: html, text
- src/htslib/vcf_sweep.c - lines changed 183, context: html, text, full: html, text
- src/htslib/vcfutils.c - lines changed 691, 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/hgTracks/bamTrack.c - lines changed 5, context: html, text, full: html, text
cc2c8b0181212e97d22db24fc67394f4c634656e Fri Apr 24 20:19:55 2026 -0700
- added htslib submodule
012294051c7f9ded1f8392899feebbebd26ead5c Fri Apr 24 22:03:38 2026 -0700
- makefile will initialize htslib submodule if needed
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
- src/submodules/htslib - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
625a5f2525117ff4c3e5a73ad73c020af9bdd1f5 Wed Apr 29 19:45:37 2026 -0700
- added README for submodules, currently just htslib
- src/submodules/README.md - lines changed 32, context: html, text, full: html, text
1fd0ab8b59002435f0da06a8c5f1525db09024dc Thu Apr 30 20:52:15 2026 -0700
- inital conversion of fetchKentSource, can not test until on github
- src/userApps/fetchKentSource.sh - 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/hg/encode3/validateFiles/validateFiles.c - lines changed 1, context: html, text, full: html, text
- src/lib/tests/expected/vcfHeader1kGNoGenotypes.out - lines changed 6, context: html, text, full: html, text
- src/lib/tests/expected/vcfHeader1kGWithGenotypes.out - lines changed 11, context: html, text, full: html, text
- src/lib/tests/expected/vcfHeaderOldV3.out - lines changed 6, context: html, text, full: html, text
- src/lib/tests/makefile - lines changed 25, context: html, text, full: html, text
- src/lib/tests/tabixFetch.c - lines changed 2, context: html, text, full: html, text
- src/lib/tests/vcfParseTest.c - lines changed 30, 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
fe875492a7da5c0f64cd9c6d43cd6809478ec2a4 Sat May 9 08:32:48 2026 -0700
- *.bai and *.tbi index files were by-passing UDC and being downloaded to current directory
437debb4d7d2cbd5cb5ead4366342aead4e7f233 Tue May 12 13:29:30 2026 -0700
- Merge remote-tracking branch 'origin/master' into htslib-driver
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
22c3e40ac360c345ab79f6bd3a51dbde33b2b4cd Tue May 12 14:25:49 2026 -0700
- move submoduleSet to submodule dir
- src/submodules/submoduleSetup - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
5049589b9025e6961a2aab60f629159033141dc2 Tue May 12 14:31:21 2026 -0700
- run topChecks before any topLibs, even if done in parallel
2655a0cce4d565ac1c1c54fcf238b49cba2c5d37 Tue May 12 14:50:08 2026 -0700
- try to make sure topCheck runs first
992012e9add85a0bd2d5fffc96d80427468893f3 Tue May 12 15:11:23 2026 -0700
- Merge branch 'htslib-driver2'
Convert bundled htslib to a git submodule and route remote BAM/VCF/tabix
access through htslib's hfile scheme-handler mechanism backed by UDC,
replacing the legacy knetUdc/knetfile hooks.
* Move htslib to src/submodules/htslib with init/check script
* Rework UDC integration via hfile driver (hfileUdc.c); knetUdcInstall
remains as a thin compatibility stub
* Fix hfile_add_scheme_handler init order so kent can register UDC
handlers before any hopen
* Route remote .bai/.tbi/.crai index reads through UDC instead of
htslib downloading copies into CWD
* Re-enable tabix VCF tests previously gated by a non-existent
USE_TABIX make variable; fix related tabix header access regression
* Initial conversion of fetchKentSource for submodule-aware checkout
* Drop UCSC-bundled static libcurl; use system libcurl
1fc1fed014272d6781d8f98845efae537e808e58 Sat May 16 20:07:30 2026 -0700
- added option to get attribute output from gtfToGenePred in TSV format
- src/hg/utils/gtfToGenePred/gtfToGenePred.c - lines changed 15, context: html, text, full: html, text
- src/hg/utils/gtfToGenePred/tests/expected/impliedStop.info - lines changed 1, context: html, text, full: html, text
- src/hg/utils/gtfToGenePred/tests/makefile - lines changed 1, context: html, text, full: html, text
683ed1ec1118d21c351579f323fa0f5760c91100 Mon May 18 05:32:11 2026 -0700
- add --llzma for non-hgwdev builds
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