Commits for kent
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v434_preview to v434_preview2 (2022-07-05 to 2022-07-11) v434
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a1cfd4eb6e2f1e0eb0e8756fd02ebcb602c77687 Tue Jun 28 13:08:30 2022 -0700
- Making base-by-base alignment display work for bigChains and bigPsls.
957e6639419c3faf3ca76d891903ea3023681555 Tue Jun 28 18:02:27 2022 -0700
- Making 'View details of parts of alignment within browser window.' link on bigPsl and psl work better when query sequence is big.
e3b577eca3df08b19af7168ac86223be72b91546 Wed Jun 29 19:05:57 2022 -0700
- Adding 2bit option to baseColorUseSequence tag.
7e6bfce5ff65b67d6e75b239c8b7fb3270f475fb Wed Jun 29 19:11:10 2022 -0700
- Making baseColorDrawItem(), baseColorOverdrawDiff(), and baseColorOverdrawQInsert() functions to from mrnaSeq parameter to qSeq/qOffset parameter pair. Currently qOffset is always zero, but have plans to use it so that not necessarily all of query sequence needs to be loaded. qSeq may be a whole chromosome for a chain.
- src/hg/hgTracks/bamTrack.c - lines changed 8, context: html, text, full: html, text
- src/hg/hgTracks/simpleTracks.c - lines changed 6, context: html, text, full: html, text
e1abdbe4945561b19dad7d4139982f511e4b2b5d Wed Jun 29 19:12:39 2022 -0700
- Expanding coloring based on query sequence to include chain tracks.
- src/hg/hgTracks/cds.c - lines changed 137, context: html, text, full: html, text
- src/hg/hgTracks/chainTrack.c - lines changed 9, context: html, text, full: html, text
- src/hg/hgTracks/hgTracks.h - lines changed 7, context: html, text, full: html, text
4f7e594f8fdbf052a0d00a6c981c55f49d054782 Thu Jun 30 11:20:59 2022 -0700
- Enabling qInsert and incomplete-matching-to-query for chains and bigChains.
76bde04179c67dde93143803a1502cb80e8abc33 Thu Jun 30 11:27:08 2022 -0700
- Making qInserts be rendered as two bases wide rather than always a single pixel line. If zoomed in enough will show size of insert in query as a number in the middle of the box. See also redmine #29642. Also qInserts are drawn after, not before, the red blocks of base mismatches.
- src/hg/hgTracks/bamTrack.c - lines changed 1, context: html, text, full: html, text
- src/hg/hgTracks/chainTrack.c - lines changed 1, context: html, text, full: html, text
- src/hg/hgTracks/simpleTracks.c - lines changed 5, context: html, text, full: html, text
c3713514c6475447ac5e1350c07c6610662fb916 Thu Jun 30 11:27:55 2022 -0700
- Adding qSize structure to linkedFeatures, the better to make psls out of it for base-by-base view of chains.
- src/hg/hgTracks/hgTracks.h - lines changed 1, context: html, text, full: html, text
cedffcafd9704d81d79381318468b85e900f2653 Thu Jun 30 15:51:07 2022 -0700
- Documenting new otherTwoBitUrl tag and addition to baseColorUseSequence tag. Also fixing little typo in bigDataUrl2 tag.
- src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html - lines changed 5, context: html, text, full: html, text
- src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html - lines changed 3, context: html, text, full: html, text
- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 14, context: html, text, full: html, text
91c4d60a5bcbf19016e3eb0fd4fdcccb2588a5b4 Thu Jun 30 19:03:04 2022 -0700
- Fixing BAM base level coloring recently introduced bug. Making the purple incompletely aligned ends be a little more visible and include the size of missing begin or end if zooomed in enough.
a27a778580784849da8b9026ef2e34a5c67a7367 Fri Jul 1 16:50:30 2022 -0700
- Seems to work. I'll fix some of the names, maybe polish it some more, before moving it out of oneShot.
- src/oneShot/testTwoBitRangeCache/testTwoBitRangeCache.c - lines changed 230, context: html, text, full: html, text
7580a364f0819e5ab6244b2b1ff685980b93c188 Fri Jul 1 18:25:00 2022 -0700
- First cut at cacheTwoBit system - which will cache pieces of two bit files we've read. System has some sense about only loading what it hasn't seen already, and only loading the part it needs to see. Could be improved, but better than storing all of each sequence.
- src/lib/cacheTwoBit.c - lines changed 175, context: html, text, full: html, text
- src/oneShot/testTwoBitRangeCache/testTwoBitRangeCache.c - lines changed 167, context: html, text, full: html, text
03270520d98b7251dc50b75c1a2815f8f5de63ec Fri Jul 1 18:37:18 2022 -0700
- Making ends with unmatched query just 2 pixels again. Need to fix some stuff before capping with anything more fancy.
be07e4273228ea43ed8f24dc076af4a633e7916f Sun Jul 3 14:58:45 2022 -0700
- Adding twoBitHasSeq function to query if a sequence exists in file.
f8458ca93f0c0abe5456789dd7a9618d63e55e5b Sun Jul 3 15:01:40 2022 -0700
- Fixing bug on reverse strand and improving cache behavior. Making it so you can ask for a cached sequence without aborting if it doesn't exist.
3d2299a0b9690e88341c660965d913ad105970f2 Sun Jul 3 15:03:16 2022 -0700
- Improving caching behavior. Allowing it to cache less than a complete sequence. Handling reverse strand better.
- src/hg/hgTracks/cds.c - lines changed 151, context: html, text, full: html, text
efc87af4e5921d966a5bbc9ce8832b7f374f4599 Mon Jul 4 17:31:44 2022 -0700
- Added file parameter to cacheTwoBitRangesPrintStats.
ae53d1dc78b4079bb3427597efe465aa7bfe6ddc Mon Jul 4 17:34:00 2022 -0700
- Changing debugging output.
- src/hg/hgTracks/hgTracks.c - lines changed 4, context: html, text, full: html, text
83670939fee1a5751c5c0b7fa58b2d2343ddb6c6 Mon Jul 4 17:35:08 2022 -0700
- Adding chain and bigChain to some of the base-by-base display tags.
- src/hg/makeDb/trackDb/tagTypes.tab - lines changed 4, context: html, text, full: html, text
cf0805c7d57bf59f29969d3b17ba7a17c57cb81e Tue Jul 5 12:59:33 2022 -0700
- Adding coloring options and otherTwoBitUrl to chains and psls.
- src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html - lines changed 17, context: html, text, full: html, text
- src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html - lines changed 32, context: html, text, full: html, text
ea5551fd4f1ea0c73e95fb5ee1f5ecd557509854 Fri Jul 8 14:06:33 2022 -0700
- Improving comments and diagnostic output.
1da73beaaf2e06a18feeb0b15f5f3786a66fb60b Fri Jul 8 14:07:23 2022 -0700
- Making little purple and green ticks at end of RNA alignments smaller like they were before.
10a07357508dcfdfcec414d5129388449eb0a083 Fri Jul 8 14:08:02 2022 -0700
- Removing debugging info to stderr on query cache.
- src/hg/hgTracks/hgTracks.c - lines changed 2, context: html, text, full: html, text
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