All File Changes

v319_base to v320_preview (2015-07-13 to 2015-07-20) v320

• cirmNotes.txt
  • lines changed 18, context: html, text, full: html, text
    removing an uncessary file that worked its way into the repo
    
• src/hg/cartDump/cartDump.c
  • lines changed 9, context: html, text, full: html, text
    fixing cartDump so that cartDump calls to update cart for track data from hgTracks and ajax.js do not get limited by bottleneck.
    
• src/hg/expMatrixToJson/expMatrixToJson.c
  • lines changed 122, context: html, text, full: html, text
    Fixed the program up a bit, documented and removed some unecessary options
    
  • lines changed 1, context: html, text, full: html, text
    Fixed a bug
    
• src/hg/hgCustom/hgCustom.c
  • lines changed 86, context: html, text, full: html, text
    Adding Data Integrator to list of destinations from the Manage Custom Tracks
    page. Since there are now 4 destinations, instead of having one button for
    each, use a menu to select the destination and a single 'go' button.
    Align the 'add custom tracks' button with the new menu.
    refs #15517
    
• src/hg/hgGene/hgGeneData/Human/hg16/links.ra
  • lines changed 1, context: html, text, full: html, text
    fixing exonprimer links, refs #15708
    
• src/hg/hgGene/hgGeneData/Human/hg17/links.ra
  • lines changed 1, context: html, text, full: html, text
    fixing exonprimer links, refs #15708
    
• src/hg/hgGene/hgGeneData/Human/hg18/links.ra
  • lines changed 2, context: html, text, full: html, text
    fixing exonprimer links, refs #15708
    
• src/hg/hgGene/hgGeneData/Human/hg19/links.ra
  • lines changed 1, context: html, text, full: html, text
    fixing exonprimer links, refs #15708
    
• src/hg/hgGene/hgGeneData/Human/hg38/links.ra
  • lines changed 1, context: html, text, full: html, text
    fixing exonprimer links, refs #15708
    
  • lines changed 6, context: html, text, full: html, text
    added ExonPrimer link #15656
    
• src/hg/hgGene/hgGeneData/Mouse/mm10/links.ra
  • lines changed 1, context: html, text, full: html, text
    fixing exonprimer links, refs #15708
    
• src/hg/hgGene/hgGeneData/Mouse/mm6/links.ra
  • lines changed 1, context: html, text, full: html, text
    fixing exonprimer links, refs #15708
    
• src/hg/hgGene/hgGeneData/Mouse/mm7/links.ra
  • lines changed 1, context: html, text, full: html, text
    fixing exonprimer links, refs #15708
    
• src/hg/hgGene/hgGeneData/Mouse/mm8/links.ra
  • lines changed 1, context: html, text, full: html, text
    fixing exonprimer links, refs #15708
    
• src/hg/hgGene/hgGeneData/Mouse/mm9/links.ra
  • lines changed 1, context: html, text, full: html, text
    fixing exonprimer links, refs #15708
    
• src/hg/hgMirror/hgMirror
  • lines changed 2, context: html, text, full: html, text
    fixing a hgMirror bug on gbib found by Hiram
    
  • lines changed 6, context: html, text, full: html, text
    fixing another hgMirror bug that Hiram found
    
  • lines changed 1, context: html, text, full: html, text
    extending the "reset" parameter to hgMirror slightly
    
  • lines changed 3, context: html, text, full: html, text
    another hgMirror fix: temp file deletion and hash bang line
    
  • lines changed 15, context: html, text, full: html, text
    fixing missing menu update in hgMirror for show subtracks, refs #15471
    
• src/hg/hgMirror/makefile
  • lines changed 4, context: html, text, full: html, text
    trying to make sure that in the future hgMirrors are caught more easily,
    by making hgwdev look more like gbib
    
  • lines changed 1, context: html, text, full: html, text
    Adding -s (silent) to curl so it doesn't report speed to stderr when we run make > /dev/null.
    
• src/hg/hgTracks/cds.c
  • lines changed 4, context: html, text, full: html, text
    Removing obsolete 8-bit color support. refs #15722
    
• src/hg/hgTracks/wigTrack.c
  • lines changed 3, context: html, text, full: html, text
    Removing obsolete 8-bit color support. refs #15722
    
• src/hg/htdocs/goldenPath/help/hgSessionHelp.html
  • lines changed 13, context: html, text, full: html, text
    changed statement that recommends saving hgTrack url after clicking a session link. That url no longer loads the session
    
• src/hg/htdocs/images/Ancylostoma_ceylanicum.jpg
  • lines changed 0, context: html, text, full: html, text
    photo from CDC public domain refs #15209
    
• src/hg/htdocs/images/Heterorhabditis_bacteriophora.jpg
  • lines changed 0, context: html, text, full: html, text
    photo from USDA/Peggy Greb refs #15209
    
• src/hg/htdocs/training/index.html
  • lines changed 1, context: html, text, full: html, text
    Adding a comment line on training/index.html refs #15703
    
  • lines changed 14, context: html, text, full: html, text
    commiting some changes that git told me to, so I can finish my git pull
    
  • lines changed 17, context: html, text, full: html, text
    dropped Texas A&M (done) and added UC Davis
    
  • lines changed 9, context: html, text, full: html, text
    added map of trainings and link to it on training/index page. refs #15730
    
• src/hg/htdocs/training/trainingMap.html
  • lines changed 58, context: html, text, full: html, text
    added map of trainings and link to it on training/index page. refs #15730
    
• src/hg/makeDb/doc/augustusGene.txt
  • lines changed 100, context: html, text, full: html, text
    indicate standard procedure refs #13088
    
  • lines changed 13, context: html, text, full: html, text
    updated db list with recent assemblies refs #13088
    
  • lines changed 7, context: html, text, full: html, text
    remove dbs that have no table or are actually not databases refs #13088
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 114, context: html, text, full: html, text
    Built snp144* tracks for hg19 and hg38. Automated the production of SNV-masked
    assembly sequence and "orthologous alleles" (i.e. liftOver of SNVs to chimp,
    orangutan and macaque & extraction of their nucleotide at that position).
    refs #15493
    
    Also added the snpNNN{Common,Flagged,Mult} tables to the snpExceptionNNN
    identifiers in all.joiner.
    refs #3606
    
• src/hg/makeDb/doc/hg38/variation.txt
  • lines changed 104, context: html, text, full: html, text
    Built snp144* tracks for hg19 and hg38. Automated the production of SNV-masked
    assembly sequence and "orthologous alleles" (i.e. liftOver of SNVs to chimp,
    orangutan and macaque & extraction of their nucleotide at that position).
    refs #15493
    
    Also added the snpNNN{Common,Flagged,Mult} tables to the snpExceptionNNN
    identifiers in all.joiner.
    refs #3606
    
• src/hg/makeDb/doc/worms/ancCey1.txt
  • lines changed 438, context: html, text, full: html, text
    starting build for Ancylostoma ceylanicum/hookworm refs #15209
    
• src/hg/makeDb/doc/worms/ascSuu1.txt
  • lines changed 451, context: html, text, full: html, text
    initial business for Ascaris suum refs #15209
    
• src/hg/makeDb/doc/worms/hetBac1.txt
  • lines changed 483, context: html, text, full: html, text
    starting build for Heterorhabditis bacteriophora/hetBac1 refs #15209
    
• src/hg/makeDb/doc/worms/necAme1.txt
  • lines changed 444, context: html, text, full: html, text
    adding build of Necator americanus/hookworm refs #15209
    
• src/hg/makeDb/doc/worms/priExs1.txt
  • lines changed 462, context: html, text, full: html, text
    starting Pristionchus exspectatus build refs #15209
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 37, context: html, text, full: html, text
    Built snp144* tracks for hg19 and hg38. Automated the production of SNV-masked
    assembly sequence and "orthologous alleles" (i.e. liftOver of SNVs to chimp,
    orangutan and macaque & extraction of their nucleotide at that position).
    refs #15493
    
    Also added the snpNNN{Common,Flagged,Mult} tables to the snpExceptionNNN
    identifiers in all.joiner.
    refs #3606
    
• src/hg/makeDb/trackDb/augustusGene.html
  • lines changed 4, context: html, text, full: html, text
    Changes based on CR, refs #15699
    
  • lines changed 2, context: html, text, full: html, text
    More changes based on CR, refs #15699
    
• src/hg/makeDb/trackDb/human/hg18/targetScanS.html
  • lines changed 14, context: html, text, full: html, text
    Changes based on CR, refs #15699
    
• src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMap.html
  • lines changed 7, context: html, text, full: html, text
    Changes based on CR, refs #15699
    
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethyl27.html
  • lines changed 13, context: html, text, full: html, text
    Changes based on CR, refs #15699
    
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 12, context: html, text, full: html, text
    Built snp144* tracks for hg19 and hg38. Automated the production of SNV-masked
    assembly sequence and "orthologous alleles" (i.e. liftOver of SNVs to chimp,
    orangutan and macaque & extraction of their nucleotide at that position).
    refs #15493
    
    Also added the snpNNN{Common,Flagged,Mult} tables to the snpExceptionNNN
    identifiers in all.joiner.
    refs #3606
    
• src/hg/makeDb/trackDb/human/hg38/knownGene.html
  • lines changed 141, context: html, text, full: html, text
    renaming of GENCODE Basic to GENCODE, html for knownGeneOld, and clean
    up of trackDb files to no longer use alpha/beta versions #14639
    
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
  • lines changed 19, context: html, text, full: html, text
    renaming of GENCODE Basic to GENCODE, html for knownGeneOld, and clean
    up of trackDb files to no longer use alpha/beta versions #14639
    
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra.alpha
  • lines changed 19, context: html, text, full: html, text
    renaming of GENCODE Basic to GENCODE, html for knownGeneOld, and clean
    up of trackDb files to no longer use alpha/beta versions #14639
    
• src/hg/makeDb/trackDb/human/hg38/knownGeneOld8.html
  • lines changed 20, context: html, text, full: html, text
    renaming of GENCODE Basic to GENCODE, html for knownGeneOld, and clean
    up of trackDb files to no longer use alpha/beta versions #14639
    
  • lines changed 7, context: html, text, full: html, text
    made a few corrections
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    fix a bug in hg38 trackDb where knownGeneOld8 had the wrong kg?ToKg?
    table #15661
    
  • lines changed 2, context: html, text, full: html, text
    renaming of GENCODE Basic to GENCODE, html for knownGeneOld, and clean
    up of trackDb files to no longer use alpha/beta versions #14639
    
  • lines changed 13, context: html, text, full: html, text
    Built snp144* tracks for hg19 and hg38. Automated the production of SNV-masked
    assembly sequence and "orthologous alleles" (i.e. liftOver of SNVs to chimp,
    orangutan and macaque & extraction of their nucleotide at that position).
    refs #15493
    
    Also added the snpNNN{Common,Flagged,Mult} tables to the snpExceptionNNN
    identifiers in all.joiner.
    refs #3606
    
• src/hg/makeDb/trackDb/human/hgdpFst.html
  • lines changed 1, context: html, text, full: html, text
    Changes based on CR, refs #15699
    
• src/hg/makeDb/trackDb/human/hgdpIhs.html
  • lines changed 1, context: html, text, full: html, text
    Changes based on CR, refs #15699
    
• src/hg/makeDb/trackDb/human/hgdpXpehh.html
  • lines changed 1, context: html, text, full: html, text
    Changes based on CR, refs #15699
    
• src/hg/makeDb/trackDb/human/snp144.html
  • lines changed 36, context: html, text, full: html, text
    Built snp144* tracks for hg19 and hg38. Automated the production of SNV-masked
    assembly sequence and "orthologous alleles" (i.e. liftOver of SNVs to chimp,
    orangutan and macaque & extraction of their nucleotide at that position).
    refs #15493
    
    Also added the snpNNN{Common,Flagged,Mult} tables to the snpExceptionNNN
    identifiers in all.joiner.
    refs #3606
    
• src/hg/makeDb/trackDb/human/snp144.shared.html
  • lines changed 470, context: html, text, full: html, text
    Built snp144* tracks for hg19 and hg38. Automated the production of SNV-masked
    assembly sequence and "orthologous alleles" (i.e. liftOver of SNVs to chimp,
    orangutan and macaque & extraction of their nucleotide at that position).
    refs #15493
    
    Also added the snpNNN{Common,Flagged,Mult} tables to the snpExceptionNNN
    identifiers in all.joiner.
    refs #3606
    
• src/hg/makeDb/trackDb/human/snp144Common.html
  • lines changed 28, context: html, text, full: html, text
    Built snp144* tracks for hg19 and hg38. Automated the production of SNV-masked
    assembly sequence and "orthologous alleles" (i.e. liftOver of SNVs to chimp,
    orangutan and macaque & extraction of their nucleotide at that position).
    refs #15493
    
    Also added the snpNNN{Common,Flagged,Mult} tables to the snpExceptionNNN
    identifiers in all.joiner.
    refs #3606
    
• src/hg/makeDb/trackDb/human/snp144Flagged.html
  • lines changed 29, context: html, text, full: html, text
    Built snp144* tracks for hg19 and hg38. Automated the production of SNV-masked
    assembly sequence and "orthologous alleles" (i.e. liftOver of SNVs to chimp,
    orangutan and macaque & extraction of their nucleotide at that position).
    refs #15493
    
    Also added the snpNNN{Common,Flagged,Mult} tables to the snpExceptionNNN
    identifiers in all.joiner.
    refs #3606
    
• src/hg/makeDb/trackDb/human/snp144Mult.html
  • lines changed 25, context: html, text, full: html, text
    Built snp144* tracks for hg19 and hg38. Automated the production of SNV-masked
    assembly sequence and "orthologous alleles" (i.e. liftOver of SNVs to chimp,
    orangutan and macaque & extraction of their nucleotide at that position).
    refs #15493
    
    Also added the snpNNN{Common,Flagged,Mult} tables to the snpExceptionNNN
    identifiers in all.joiner.
    refs #3606
    
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 107, context: html, text, full: html, text
    Built snp144* tracks for hg19 and hg38. Automated the production of SNV-masked
    assembly sequence and "orthologous alleles" (i.e. liftOver of SNVs to chimp,
    orangutan and macaque & extraction of their nucleotide at that position).
    refs #15493
    
    Also added the snpNNN{Common,Flagged,Mult} tables to the snpExceptionNNN
    identifiers in all.joiner.
    refs #3606
    
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding Ascaris suum/Pig roundworm to build refs #15209
    
  • lines changed 1, context: html, text, full: html, text
    adding Pristionchus exspectatus/priExs1 to the build refs #15209
    
  • lines changed 1, context: html, text, full: html, text
    adding Heterorhabditis bacteriophora/hetBac1 to the build refs #15209
    
  • lines changed 1, context: html, text, full: html, text
    adding Ancylostoma ceylanicum/hookworm refs #15209
    
  • lines changed 1, context: html, text, full: html, text
    adding Necator americanus/hookworm/necAme1 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/ancCey1/description.html
  • lines changed 63, context: html, text, full: html, text
    adding Ancylostoma ceylanicum/hookworm refs #15209
    
• src/hg/makeDb/trackDb/worm/ancCey1/gap.html
  • lines changed 30, context: html, text, full: html, text
    adding Ancylostoma ceylanicum/hookworm refs #15209
    
• src/hg/makeDb/trackDb/worm/ancCey1/gold.html
  • lines changed 33, context: html, text, full: html, text
    adding Ancylostoma ceylanicum/hookworm refs #15209
    
• src/hg/makeDb/trackDb/worm/ancCey1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding Ancylostoma ceylanicum/hookworm refs #15209
    
  • lines changed 5, context: html, text, full: html, text
    adding gold table search rule refs #15209
    
• src/hg/makeDb/trackDb/worm/ascSuu1/description.html
  • lines changed 63, context: html, text, full: html, text
    adding Ascaris suum/Pig roundworm to build refs #15209
    
• src/hg/makeDb/trackDb/worm/ascSuu1/gap.html
  • lines changed 30, context: html, text, full: html, text
    adding Ascaris suum/Pig roundworm to build refs #15209
    
• src/hg/makeDb/trackDb/worm/ascSuu1/gold.html
  • lines changed 34, context: html, text, full: html, text
    adding Ascaris suum/Pig roundworm to build refs #15209
    
• src/hg/makeDb/trackDb/worm/ascSuu1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding Ascaris suum/Pig roundworm to build refs #15209
    
  • lines changed 6, context: html, text, full: html, text
    adding gold table search rule refs #15209
    
• src/hg/makeDb/trackDb/worm/hetBac1/description.html
  • lines changed 63, context: html, text, full: html, text
    adding Heterorhabditis bacteriophora/hetBac1 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/hetBac1/gap.html
  • lines changed 30, context: html, text, full: html, text
    adding Heterorhabditis bacteriophora/hetBac1 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/hetBac1/gold.html
  • lines changed 34, context: html, text, full: html, text
    adding Heterorhabditis bacteriophora/hetBac1 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/hetBac1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding Heterorhabditis bacteriophora/hetBac1 to the build refs #15209
    
  • lines changed 5, context: html, text, full: html, text
    adding gold table search rule refs #15209
    
• src/hg/makeDb/trackDb/worm/necAme1/description.html
  • lines changed 63, context: html, text, full: html, text
    adding Necator americanus/hookworm/necAme1 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/necAme1/gap.html
  • lines changed 30, context: html, text, full: html, text
    adding Necator americanus/hookworm/necAme1 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/necAme1/gold.html
  • lines changed 34, context: html, text, full: html, text
    adding Necator americanus/hookworm/necAme1 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/necAme1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding Necator americanus/hookworm/necAme1 to the build refs #15209
    
  • lines changed 5, context: html, text, full: html, text
    adding gold table search rule refs #15209
    
• src/hg/makeDb/trackDb/worm/priExs1/description.html
  • lines changed 63, context: html, text, full: html, text
    adding Pristionchus exspectatus/priExs1 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/priExs1/gap.html
  • lines changed 31, context: html, text, full: html, text
    adding Pristionchus exspectatus/priExs1 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/priExs1/gold.html
  • lines changed 33, context: html, text, full: html, text
    adding Pristionchus exspectatus/priExs1 to the build refs #15209
    
• src/hg/makeDb/trackDb/worm/priExs1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding Pristionchus exspectatus/priExs1 to the build refs #15209
    
  • lines changed 6, context: html, text, full: html, text
    adding gold track search rule refs #15209
    
• src/hg/makeDb/trackDb/xenTro/xenTro3/description.html
  • lines changed 1, context: html, text, full: html, text
    Changes based on CR, refs #15699
    
• src/hg/utils/automation/categorizeSnps.pl
  • lines changed 3, context: html, text, full: html, text
    Built snp144* tracks for hg19 and hg38. Automated the production of SNV-masked
    assembly sequence and "orthologous alleles" (i.e. liftOver of SNVs to chimp,
    orangutan and macaque & extraction of their nucleotide at that position).
    refs #15493
    
    Also added the snpNNN{Common,Flagged,Mult} tables to the snpExceptionNNN
    identifiers in all.joiner.
    refs #3606
    
• src/hg/utils/automation/doDbSnp.pl
  • lines changed 11, context: html, text, full: html, text
    Built snp144* tracks for hg19 and hg38. Automated the production of SNV-masked
    assembly sequence and "orthologous alleles" (i.e. liftOver of SNVs to chimp,
    orangutan and macaque & extraction of their nucleotide at that position).
    refs #15493
    
    Also added the snpNNN{Common,Flagged,Mult} tables to the snpExceptionNNN
    identifiers in all.joiner.
    refs #3606
    
• src/hg/utils/automation/doDbSnpMaskSequence.pl
  • lines changed 271, context: html, text, full: html, text
    Built snp144* tracks for hg19 and hg38. Automated the production of SNV-masked
    assembly sequence and "orthologous alleles" (i.e. liftOver of SNVs to chimp,
    orangutan and macaque & extraction of their nucleotide at that position).
    refs #15493
    
    Also added the snpNNN{Common,Flagged,Mult} tables to the snpExceptionNNN
    identifiers in all.joiner.
    refs #3606
    
• src/hg/utils/automation/doDbSnpOrthoAlleles.pl
  • lines changed 309, context: html, text, full: html, text
    Built snp144* tracks for hg19 and hg38. Automated the production of SNV-masked
    assembly sequence and "orthologous alleles" (i.e. liftOver of SNVs to chimp,
    orangutan and macaque & extraction of their nucleotide at that position).
    refs #15493
    
    Also added the snpNNN{Common,Flagged,Mult} tables to the snpExceptionNNN
    identifiers in all.joiner.
    refs #3606
    
• src/hg/utils/automation/joinOrthoAlleles.csh
  • lines changed 54, context: html, text, full: html, text
    Built snp144* tracks for hg19 and hg38. Automated the production of SNV-masked
    assembly sequence and "orthologous alleles" (i.e. liftOver of SNVs to chimp,
    orangutan and macaque & extraction of their nucleotide at that position).
    refs #15493
    
    Also added the snpNNN{Common,Flagged,Mult} tables to the snpExceptionNNN
    identifiers in all.joiner.
    refs #3606
    
• src/hg/utils/automation/snpAddTGPAlleleFreq.pl
  • lines changed 30, context: html, text, full: html, text
    Built snp144* tracks for hg19 and hg38. Automated the production of SNV-masked
    assembly sequence and "orthologous alleles" (i.e. liftOver of SNVs to chimp,
    orangutan and macaque & extraction of their nucleotide at that position).
    refs #15493
    
    Also added the snpNNN{Common,Flagged,Mult} tables to the snpExceptionNNN
    identifiers in all.joiner.
    refs #3606
    
• src/inc/common.mk
  • lines changed 5, context: html, text, full: html, text
    Removing obsolete 8-bit color support. refs #15722
    
• src/inc/memgfx.h
  • lines changed 17, context: html, text, full: html, text
    Removing obsolete 8-bit color support. refs #15722
    
• src/lib/memgfx.c
  • lines changed 87, context: html, text, full: html, text
    Removing obsolete 8-bit color support. refs #15722
    
• src/lib/pngwrite.c
  • lines changed 20, context: html, text, full: html, text
    Removing obsolete 8-bit color support. refs #15722
    
• src/lib/pscmGfx.c
  • lines changed 81, context: html, text, full: html, text
    Removing obsolete 8-bit color support. refs #15722
    
• src/lib/vGif.c
  • lines changed 66, context: html, text, full: html, text
    Removing obsolete 8-bit color support. refs #15722
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v320 preview1 refs #15731
    

• lines changed: 5692
• files changed: 111