File Changes for angie

v367_base to v368_preview (2018-06-18 to 2018-06-25) v368

• src/hg/hgLiftOver/hgLiftOver.c
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    5dd57ba4756985d35f8ca72756d963b77934fcf0 Thu Jun 7 16:08:53 2018 -0700
    Expand support for -multiple to BED 3 to 12 (instead of 4 to 6). refs #18853 Added a -noSerial option to prevent -multiple from forcing the score field to contain a serial number for BED without blocks. Also fixed a bug with the loop on chains overwriting args thickStart and thickEnd. Todo: genePred. Probably won't bother doing PSL because pslMap should be used for that. Also removed some very old #ifdef'd code.
• src/hg/hgTracks/hgTracks.c
  • lines changed 15, context: html, text, full: html, text
    082f118d6f5d17754c5fafd8d95f700c9397d99e Thu Jun 21 11:10:32 2018 -0700
    Update multi-region haplotype mode to work with _fix patch sequences in addition to _alt sequences. refs #18854
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    5dd57ba4756985d35f8ca72756d963b77934fcf0 Thu Jun 7 16:08:53 2018 -0700
    Expand support for -multiple to BED 3 to 12 (instead of 4 to 6). refs #18853 Added a -noSerial option to prevent -multiple from forcing the score field to contain a serial number for BED without blocks. Also fixed a bug with the loop on chains overwriting args thickStart and thickEnd. Todo: genePred. Probably won't bother doing PSL because pslMap should be used for that. Also removed some very old #ifdef'd code.
• src/hg/hgTracks/menu.c
  • lines changed 1, context: html, text, full: html, text
    5dd57ba4756985d35f8ca72756d963b77934fcf0 Thu Jun 7 16:08:53 2018 -0700
    Expand support for -multiple to BED 3 to 12 (instead of 4 to 6). refs #18853 Added a -noSerial option to prevent -multiple from forcing the score field to contain a serial number for BED without blocks. Also fixed a bug with the loop on chains overwriting args thickStart and thickEnd. Todo: genePred. Probably won't bother doing PSL because pslMap should be used for that. Also removed some very old #ifdef'd code.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    5dd57ba4756985d35f8ca72756d963b77934fcf0 Thu Jun 7 16:08:53 2018 -0700
    Expand support for -multiple to BED 3 to 12 (instead of 4 to 6). refs #18853 Added a -noSerial option to prevent -multiple from forcing the score field to contain a serial number for BED without blocks. Also fixed a bug with the loop on chains overwriting args thickStart and thickEnd. Todo: genePred. Probably won't bother doing PSL because pslMap should be used for that. Also removed some very old #ifdef'd code.
• src/hg/hgc/peakClusters.c
  • lines changed 2, context: html, text, full: html, text
    2fd1f4e705f129be8654845b0ca452862706cd06 Fri Jun 15 17:13:32 2018 -0700
    corner case: hFreeConn was not called when a peakClusters input track table doesn't exist, leading to 'too many connections' error when none of the input tables exist
• src/hg/inc/liftOver.h
  • lines changed 4, context: html, text, full: html, text
    5dd57ba4756985d35f8ca72756d963b77934fcf0 Thu Jun 7 16:08:53 2018 -0700
    Expand support for -multiple to BED 3 to 12 (instead of 4 to 6). refs #18853 Added a -noSerial option to prevent -multiple from forcing the score field to contain a serial number for BED without blocks. Also fixed a bug with the loop on chains overwriting args thickStart and thickEnd. Todo: genePred. Probably won't bother doing PSL because pslMap should be used for that. Also removed some very old #ifdef'd code.
• src/hg/lib/gtexGeneBed.c
  • lines changed 3, context: html, text, full: html, text
    51bd7d1443d629518ab0f9beed9b2c223a6342ae Mon Jun 18 14:19:44 2018 -0700
    gtexGeneBed.sql used PRIMARY KEY(geneId), which excluded nearly all mappings to chr*_alt. Change it to (chrom,geneId) to allow mapping to multiple sequences. refs #18853
• src/hg/lib/gtexGeneBed.sql
  • lines changed 2, context: html, text, full: html, text
    51bd7d1443d629518ab0f9beed9b2c223a6342ae Mon Jun 18 14:19:44 2018 -0700
    gtexGeneBed.sql used PRIMARY KEY(geneId), which excluded nearly all mappings to chr*_alt. Change it to (chrom,geneId) to allow mapping to multiple sequences. refs #18853
• src/hg/lib/liftOver.c
  • lines changed 306, context: html, text, full: html, text
    5dd57ba4756985d35f8ca72756d963b77934fcf0 Thu Jun 7 16:08:53 2018 -0700
    Expand support for -multiple to BED 3 to 12 (instead of 4 to 6). refs #18853 Added a -noSerial option to prevent -multiple from forcing the score field to contain a serial number for BED without blocks. Also fixed a bug with the loop on chains overwriting args thickStart and thickEnd. Todo: genePred. Probably won't bother doing PSL because pslMap should be used for that. Also removed some very old #ifdef'd code.
• src/hg/liftOver/liftOver.c
  • lines changed 11, context: html, text, full: html, text
    5dd57ba4756985d35f8ca72756d963b77934fcf0 Thu Jun 7 16:08:53 2018 -0700
    Expand support for -multiple to BED 3 to 12 (instead of 4 to 6). refs #18853 Added a -noSerial option to prevent -multiple from forcing the score field to contain a serial number for BED without blocks. Also fixed a bug with the loop on chains overwriting args thickStart and thickEnd. Todo: genePred. Probably won't bother doing PSL because pslMap should be used for that. Also removed some very old #ifdef'd code.
• src/hg/makeDb/doc/grcHhh38/grcH38P11.lastzRuns.txt
  • lines changed 11191, context: html, text, full: html, text
    0bf6af3ae38aea8ce09f24d41a75e0cae189ad95 Mon Jun 25 08:51:37 2018 -0700
    Experimental work in preparation for adding patch sequences to an existing database: not-for-release databases grcHhh38 and grcH38P11. refs #18853 grcHhh38 initialBuild used hg38 sequences and added a few basic tracks, mostly copied from hg38. grcH38P11 is a patches-only build of GRCh38.p11, similar to Hiram's hg38Patch11, but with a couple extra steps to make it a full browsable database with the usual directory structure for building tracks such as chain/net. patchUpdate.11.txt is the process for adding patch sequences (from grcH38P11) to an existing database (grcHhh38) and adding annotations on patch sequences to existing annotation tracks.
• src/hg/makeDb/doc/grcHhh38/grcH38P11.txt
  • lines changed 475, context: html, text, full: html, text
    0bf6af3ae38aea8ce09f24d41a75e0cae189ad95 Mon Jun 25 08:51:37 2018 -0700
    Experimental work in preparation for adding patch sequences to an existing database: not-for-release databases grcHhh38 and grcH38P11. refs #18853 grcHhh38 initialBuild used hg38 sequences and added a few basic tracks, mostly copied from hg38. grcH38P11 is a patches-only build of GRCh38.p11, similar to Hiram's hg38Patch11, but with a couple extra steps to make it a full browsable database with the usual directory structure for building tracks such as chain/net. patchUpdate.11.txt is the process for adding patch sequences (from grcH38P11) to an existing database (grcHhh38) and adding annotations on patch sequences to existing annotation tracks.
• src/hg/makeDb/doc/grcHhh38/initialBuild.txt
  • lines changed 512, context: html, text, full: html, text
    0bf6af3ae38aea8ce09f24d41a75e0cae189ad95 Mon Jun 25 08:51:37 2018 -0700
    Experimental work in preparation for adding patch sequences to an existing database: not-for-release databases grcHhh38 and grcH38P11. refs #18853 grcHhh38 initialBuild used hg38 sequences and added a few basic tracks, mostly copied from hg38. grcH38P11 is a patches-only build of GRCh38.p11, similar to Hiram's hg38Patch11, but with a couple extra steps to make it a full browsable database with the usual directory structure for building tracks such as chain/net. patchUpdate.11.txt is the process for adding patch sequences (from grcH38P11) to an existing database (grcHhh38) and adding annotations on patch sequences to existing annotation tracks.
• src/hg/makeDb/doc/grcHhh38/patchUpdate.11.txt
  • lines changed 591, context: html, text, full: html, text
    0bf6af3ae38aea8ce09f24d41a75e0cae189ad95 Mon Jun 25 08:51:37 2018 -0700
    Experimental work in preparation for adding patch sequences to an existing database: not-for-release databases grcHhh38 and grcH38P11. refs #18853 grcHhh38 initialBuild used hg38 sequences and added a few basic tracks, mostly copied from hg38. grcH38P11 is a patches-only build of GRCh38.p11, similar to Hiram's hg38Patch11, but with a couple extra steps to make it a full browsable database with the usual directory structure for building tracks such as chain/net. patchUpdate.11.txt is the process for adding patch sequences (from grcH38P11) to an existing database (grcHhh38) and adding annotations on patch sequences to existing annotation tracks.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 14, context: html, text, full: html, text
    79b4b0c9b07ec4bad8687b6c0f63bbd6b1805655 Fri May 11 09:15:40 2018 -0700
    Ran same-species liftOver with chainBridge through net stage for comparison with existing hg19ToHg38.over.chain. refs #21651
• src/hg/mouseStuff/chainBridge/chainBridge.c
  • lines changed 397, context: html, text, full: html, text
    fdd9aae7db69e2c910f0a2cb0dc1fea0fc00f3cd Thu May 31 12:35:34 2018 -0700
    New program chainBridge (refs #21651): try to bridge double-sided gaps in chains, first by trivially extending over perfect matches if possible, then by banded S-W alignment if gap sizes are similar on t and q and not too large. This is useful for fixing up some double-sided gaps that skip identical or nearly identical sequences found in some of our liftOver chain files. In doSameSpeciesLiftOver.pl, pipe axtChain to chainBridge.
• src/hg/mouseStuff/chainBridge/makefile
  • lines changed 4, context: html, text, full: html, text
    fdd9aae7db69e2c910f0a2cb0dc1fea0fc00f3cd Thu May 31 12:35:34 2018 -0700
    New program chainBridge (refs #21651): try to bridge double-sided gaps in chains, first by trivially extending over perfect matches if possible, then by banded S-W alignment if gap sizes are similar on t and q and not too large. This is useful for fixing up some double-sided gaps that skip identical or nearly identical sequences found in some of our liftOver chain files. In doSameSpeciesLiftOver.pl, pipe axtChain to chainBridge.
• src/hg/mouseStuff/makefile
  • lines changed 1, context: html, text, full: html, text
    fdd9aae7db69e2c910f0a2cb0dc1fea0fc00f3cd Thu May 31 12:35:34 2018 -0700
    New program chainBridge (refs #21651): try to bridge double-sided gaps in chains, first by trivially extending over perfect matches if possible, then by banded S-W alignment if gap sizes are similar on t and q and not too large. This is useful for fixing up some double-sided gaps that skip identical or nearly identical sequences found in some of our liftOver chain files. In doSameSpeciesLiftOver.pl, pipe axtChain to chainBridge.
• src/hg/utils/agpAlign/agpAlign.c
  • lines changed 240, context: html, text, full: html, text
    1e47ca9f2acedf205f065ca259bef14f2b5bf6cc Mon May 14 17:03:49 2018 -0700
    New program agpAlign.c (not yet in top-level build) finds common contigs between assemblies. refs #21650
• src/hg/utils/agpAlign/makefile
  • lines changed 3, context: html, text, full: html, text
    1e47ca9f2acedf205f065ca259bef14f2b5bf6cc Mon May 14 17:03:49 2018 -0700
    New program agpAlign.c (not yet in top-level build) finds common contigs between assemblies. refs #21650
• src/hg/utils/automation/altScaffoldPlacementToBed.pl
  • lines changed 33, context: html, text, full: html, text
    ed8466aff18192993a02770c43028f77e211130f Fri Jun 15 17:18:39 2018 -0700
    Convert NCBI assembly's alt_scaffold_placement.txt file format to altLocations.bed format. refs #18853
• src/hg/utils/automation/doBlastzChainNet.pl
  • lines changed 2, context: html, text, full: html, text
    7f802759855f5b0e0bb868d761620ade936d9562 Wed Jun 13 13:39:04 2018 -0700
    Allow doBlastzChainNet.pl to run on patch-only databases. refs #18853
• src/hg/utils/automation/doSameSpeciesLiftOver.pl
  • lines changed 3, context: html, text, full: html, text
    fdd9aae7db69e2c910f0a2cb0dc1fea0fc00f3cd Thu May 31 12:35:34 2018 -0700
    New program chainBridge (refs #21651): try to bridge double-sided gaps in chains, first by trivially extending over perfect matches if possible, then by banded S-W alignment if gap sizes are similar on t and q and not too large. This is useful for fixing up some double-sided gaps that skip identical or nearly identical sequences found in some of our liftOver chain files. In doSameSpeciesLiftOver.pl, pipe axtChain to chainBridge.
• src/hg/utils/liftOverBigWig
  • lines changed 34, context: html, text, full: html, text
    a87327b5ef28209e7a809728fb3bc8fb476dfdb8 Fri Jun 15 15:17:01 2018 -0700
    Adding liftOverBigWig for lifting from one assembly to another, and liftOverBigWigToPatches for lifting main chromosome scores to patch sequences and concatenating the results onto the original annotations. refs #18853
• src/hg/utils/liftOverBigWigToPatches
  • lines changed 40, context: html, text, full: html, text
    a87327b5ef28209e7a809728fb3bc8fb476dfdb8 Fri Jun 15 15:17:01 2018 -0700
    Adding liftOverBigWig for lifting from one assembly to another, and liftOverBigWigToPatches for lifting main chromosome scores to patch sequences and concatenating the results onto the original annotations. refs #18853
• src/oneShot/testBandExt/testBandExt.c
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    4bdf667d97956ba22278152ffff7eeff7a095a11 Tue May 15 11:08:26 2018 -0700
    Fix compiler warning about printf too few args -- doesn't affect top-level build.