File Changes for kent

v433_preview2 to v433_base (2022-06-20 to 2022-06-27) v433

• src/hg/hgTracks/bamTrack.c
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    50461aa0137fb4d85bcb2566e441f1b582594401 Wed Jun 22 20:37:43 2022 -0700
    Removing calls to baseColorDrawCleanup.
• src/hg/hgTracks/cds.c
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    2b789d0cc2a1f7c5d287820c20d2039a77a16009 Wed Jun 22 20:45:03 2022 -0700
    Removing baseColorDrawCleanup. Adding "2bit" type to baseColorUseSequence trackDb setting. Adding otherTwoBitUrl tag to trackDb. Enabling psl and bitPsl to use "baseColorDrawCLeanup 2bit" and "otherTwoBitUrl someTwoBitUrl.2bit" combination to get differing bases to be hilit in red and displaying bases when zoomed in to base level.
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    1728b2a32c308745358df39a8f25c1a8e8cbfad9 Thu Jun 23 13:39:00 2022 -0700
    Oops, fixing a NULL check I missed that was leading to crashs. #29585
• src/hg/hgTracks/cds.h
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    2b789d0cc2a1f7c5d287820c20d2039a77a16009 Wed Jun 22 20:45:03 2022 -0700
    Removing baseColorDrawCleanup. Adding "2bit" type to baseColorUseSequence trackDb setting. Adding otherTwoBitUrl tag to trackDb. Enabling psl and bitPsl to use "baseColorDrawCLeanup 2bit" and "otherTwoBitUrl someTwoBitUrl.2bit" combination to get differing bases to be hilit in red and displaying bases when zoomed in to base level.
• src/hg/hgTracks/simpleTracks.c
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    ca03872563e0ec57aef2d4214d9ac1361b0cbb86 Wed Jun 22 20:46:11 2022 -0700
    Removing call to baseColorDrawCleanup()
• src/hg/makeDb/trackDb/tagTypes.tab
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    5f4d3d1d62d21db2e0ca873be3d0b4779166c1f5 Wed Jun 22 20:36:35 2022 -0700
    Adding otherTwoBitUrl tag.
• src/hg/oneShot/refGraphTest/makefile
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    95df32e007a5dbe0e8bfe718fbb46f970e045050 Wed Jun 15 14:25:04 2022 -0700
    Some experimental work that has let me know where the alt-haplotypes land on the main chromosomes.
• src/hg/oneShot/refGraphTest/refGraphTest.c
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    95df32e007a5dbe0e8bfe718fbb46f970e045050 Wed Jun 15 14:25:04 2022 -0700
    Some experimental work that has let me know where the alt-haplotypes land on the main chromosomes.
• src/hg/oneShot/testLiftRechainer/makefile
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    29f88e9827e33081a9e4c4db1c6dcca6542f7ccd Sun Jun 19 22:29:39 2022 -0700
    First cut of next generation liftOver chain maker. This one is meant to handle swapping in alternate haplotypes properly, even when, as is the case with the HLA locus in the t2t, more than one alt is moved. Still needs lots of testing and polishing, but finishes and makes something semi-plausable on t2t's chr6 going against hg38's chr6 + alts.
• src/hg/oneShot/testLiftRechainer/testLiftRechainer.c
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    29f88e9827e33081a9e4c4db1c6dcca6542f7ccd Sun Jun 19 22:29:39 2022 -0700
    First cut of next generation liftOver chain maker. This one is meant to handle swapping in alternate haplotypes properly, even when, as is the case with the HLA locus in the t2t, more than one alt is moved. Still needs lots of testing and polishing, but finishes and makes something semi-plausable on t2t's chr6 going against hg38's chr6 + alts.
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    c9941d5c3c0198fea692d72db7fa44a711858598 Mon Jun 20 13:51:30 2022 -0700
    Fixing off by one bug in traceback
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    6c0adf59ef794e2a107de7cbf638041158dc406e Mon Jun 20 17:35:31 2022 -0700
    Fixed crash bug. Improved status reporting. Removed some debugging statements.
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    6557cfc305545ee5c43930fb7548b3310061c2d6 Wed Jun 22 20:32:53 2022 -0700
    First full genome functioning build of dynamic programming version to pick best chains to use for liftOver purposes out of a a pairwise genome alignment to allow best liftovers from query to target maximizing coverage of target while minimizing coverage of query. An improvement over the greedy algorithm used in netChain/chainNetSubset.
• src/inc/localmem.h
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    345e4ee67a3c7afb41be7899635259f8745fefe3 Sat Jun 18 06:31:46 2022 -0700
    Adding lmSlRef function.
• src/inc/rangeTree.h
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    31857342d47d49372089fe3b5aa802932313f3ef Sat Jun 18 06:30:38 2022 -0700
    Fixed bug in rangeTreeAddToCoverageDepth. Added parallel rangeTreeAddToCoverageList.
• src/lib/localmem.c
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    345e4ee67a3c7afb41be7899635259f8745fefe3 Sat Jun 18 06:31:46 2022 -0700
    Adding lmSlRef function.
• src/lib/rangeTree.c
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    31857342d47d49372089fe3b5aa802932313f3ef Sat Jun 18 06:30:38 2022 -0700
    Fixed bug in rangeTreeAddToCoverageDepth. Added parallel rangeTreeAddToCoverageList.