All File Changes
v339_base to v340_preview (2016-09-26 to 2016-10-03) v340
Show details
- src/hg/cirm/cdw/cdwSubmit/cdwSubmit.c
- lines changed 1, context: html, text, full: html, text
70e364792b494cc52b131d52634aed40284498e1 Tue Sep 27 12:33:17 2016 -0700
Putting in an error message if the CIRM environment is not set, refs #17334
- src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
- lines changed 93, context: html, text, full: html, text
30488513643e46306a3424c9b8b3b7e6141fe1c8 Wed Sep 21 13:49:18 2016 -0700
some changes to put in the joint data sets
- lines changed 1, context: html, text, full: html, text
84d06c9d4878d8af452d60a1b908d526fd7843e9 Tue Sep 27 12:31:35 2016 -0700
Fixing a small bug with the query page, refs #17334
- src/hg/hgTracks/hgTracks.c
- lines changed 14, context: html, text, full: html, text
3b70ea59a370e40497a20d96b18908345f5f597a Tue Sep 27 11:53:26 2016 -0700
add disconnect button to group headers that are made from hubs
- src/hg/hgTracks/wigMafTrack.c
- lines changed 19, context: html, text, full: html, text
7b89c304567373d9f309086a965706dcaa2a7670 Wed Sep 28 15:49:42 2016 -0700
if there is a maf with just the default species, use that instead of the
main maf
- lines changed 7, context: html, text, full: html, text
0268341f3b2ad1ed31c6dfee5a23f3035355f1ea Wed Sep 28 18:41:27 2016 -0700
use default maf in dense and squish modes
- src/hg/hgVai/hgVai.c
- lines changed 3, context: html, text, full: html, text
3640a4d6b3303a6bebc7c5b2fc5abcf7f4fae0b2 Wed Sep 28 11:56:00 2016 -0700
Partial support for changes in VCF4.2 and latest samtools mpileup output:
- Tolerate 'Number=R' and new INFO attributes Source and Version
- Tolerate mpileup's '<X>' alt (no alternate allele was observed)
- The 4.3 spec includes '<*>' from gVCF, also meaning no alt al obsvd.
- GT is no longer required; user's example has PL instead, so parse that
into genotypes.
- hgVai now annotates "variants" with <X> and <*> as no_sequence_alteration
- annoFormatVep now uses html encoding for html output in various places so
that "<X>" is displayed properly (custom track labels and various item
names could also have undesirable characters). I am not encoding the
extras' descriptions because those are internal and some have <a>'s.
refs #15625
- src/hg/hgc/hgc.c
- lines changed 16, context: html, text, full: html, text
7bc1475cf09a8da21c7cfa2e233f853700524200 Tue Sep 27 11:10:23 2016 -0700
ncbiRefSeqLink now has empty strings instead of n/a refs #13673
- lines changed 14, context: html, text, full: html, text
2ab031187ac37e8f7b16de41a771e6852c4f7030 Tue Sep 27 19:39:06 2016 -0700
fixed cases were cgi encoding was done at higher levels
and hence double encode in my previous change.
- lines changed 25, context: html, text, full: html, text
482d00125fb0fcdf3097ed02cf06fde08331f557 Wed Sep 28 22:48:14 2016 -0700
avoid trouble when there is no RNA sequence for an item in the ncbiRefSeq track refs #13673
- src/hg/htdocs/ebolaPortal/index.html
- lines changed 7, context: html, text, full: html, text
e06f0b8c8055093e52aadfe195d539bcb3bda74f Wed Sep 28 09:01:05 2016 -0700
Added link to downloads from Ebola portal page. Added link to portal from ebola gateway description page. refs #18149
- src/hg/htdocs/goldenPath/help/trackDb/README.txt
- lines changed 40, context: html, text, full: html, text
42e48b3e1317e1db65173c73e188f36aecfd3a22 Thu Sep 29 16:04:25 2016 -0700
Adding some hints about our trackDbLibrary.shtml trackDbHub.v#.html process to existing README in htdocs refs #10015
- src/hg/htdocs/images/newBlueHelix3.jpg
- lines changed 0, context: html, text, full: html, text
c629a73fda349ae2a746238a10252299c592f5b6 Tue Sep 27 12:19:54 2016 -0700
changing image on main index page to better reflect the molecular structure of DNA (10, not 20 bp per turn)
- lines changed 0, context: html, text, full: html, text
e247788342e72170e1c9286c9eb950a97ce29714 Thu Sep 29 13:34:19 2016 -0700
changed newBlueHelix image to be a bit darker per kate and jim and angie. using same filename
- src/hg/htdocs/index.html
- lines changed 1, context: html, text, full: html, text
c629a73fda349ae2a746238a10252299c592f5b6 Tue Sep 27 12:19:54 2016 -0700
changing image on main index page to better reflect the molecular structure of DNA (10, not 20 bp per turn)
- lines changed 1, context: html, text, full: html, text
eaef2d170ea8b272234e9b3bf453cfccf98a5ba0 Fri Sep 30 11:25:40 2016 -0700
Fixing needed encoding of pipe char in URL. refs #18077.
- lines changed 1, context: html, text, full: html, text
2e2953ca15534bf34e976f0da2f3f9aee11b7393 Fri Sep 30 12:46:45 2016 -0700
Fixing needed encoding of pipe colon comma chars in URL. refs #18077.
- src/hg/inc/annoGratorGpVar.h
- lines changed 3, context: html, text, full: html, text
3640a4d6b3303a6bebc7c5b2fc5abcf7f4fae0b2 Wed Sep 28 11:56:00 2016 -0700
Partial support for changes in VCF4.2 and latest samtools mpileup output:
- Tolerate 'Number=R' and new INFO attributes Source and Version
- Tolerate mpileup's '<X>' alt (no alternate allele was observed)
- The 4.3 spec includes '<*>' from gVCF, also meaning no alt al obsvd.
- GT is no longer required; user's example has PL instead, so parse that
into genotypes.
- hgVai now annotates "variants" with <X> and <*> as no_sequence_alteration
- annoFormatVep now uses html encoding for html output in various places so
that "<X>" is displayed properly (custom track labels and various item
names could also have undesirable characters). I am not encoding the
extras' descriptions because those are internal and some have <a>'s.
refs #15625
- src/hg/inc/hgHgvs.h
- lines changed 17, context: html, text, full: html, text
a1c329068ad18aa4093972b501e6324f8bcdb398 Fri Sep 16 17:19:30 2016 -0700
Parse HGVS position ranges and coding terms' UTR and intron coordinates.
When the chromAlias table is present, this also now supports NC_*:g. terms.
The sequence change part is no longer parsed -- it's not necessary for mapping
to genomic ranges, although it will be necessary in order for hgVai to take
HGVS input.
This does not yet support ranges-of-ranges but neither does Mutalyzer. This
also doesn't support uncertain positions ('?'). Like complex sequence changes,
those can wait until we have a sophisticated parser.
We also support some new not-quite-HGVS forms: geneSymbol and protein pos only,
or geneSymbol and c.<valid position range>.
refs #15071
- src/hg/inc/soTerm.h
- lines changed 1, context: html, text, full: html, text
3640a4d6b3303a6bebc7c5b2fc5abcf7f4fae0b2 Wed Sep 28 11:56:00 2016 -0700
Partial support for changes in VCF4.2 and latest samtools mpileup output:
- Tolerate 'Number=R' and new INFO attributes Source and Version
- Tolerate mpileup's '<X>' alt (no alternate allele was observed)
- The 4.3 spec includes '<*>' from gVCF, also meaning no alt al obsvd.
- GT is no longer required; user's example has PL instead, so parse that
into genotypes.
- hgVai now annotates "variants" with <X> and <*> as no_sequence_alteration
- annoFormatVep now uses html encoding for html output in various places so
that "<X>" is displayed properly (custom track labels and various item
names could also have undesirable characters). I am not encoding the
extras' descriptions because those are internal and some have <a>'s.
refs #15625
- src/hg/lib/annoFormatVep.c
- lines changed 52, context: html, text, full: html, text
3640a4d6b3303a6bebc7c5b2fc5abcf7f4fae0b2 Wed Sep 28 11:56:00 2016 -0700
Partial support for changes in VCF4.2 and latest samtools mpileup output:
- Tolerate 'Number=R' and new INFO attributes Source and Version
- Tolerate mpileup's '<X>' alt (no alternate allele was observed)
- The 4.3 spec includes '<*>' from gVCF, also meaning no alt al obsvd.
- GT is no longer required; user's example has PL instead, so parse that
into genotypes.
- hgVai now annotates "variants" with <X> and <*> as no_sequence_alteration
- annoFormatVep now uses html encoding for html output in various places so
that "<X>" is displayed properly (custom track labels and various item
names could also have undesirable characters). I am not encoding the
extras' descriptions because those are internal and some have <a>'s.
refs #15625
- src/hg/lib/annoGratorGpVar.c
- lines changed 5, context: html, text, full: html, text
3640a4d6b3303a6bebc7c5b2fc5abcf7f4fae0b2 Wed Sep 28 11:56:00 2016 -0700
Partial support for changes in VCF4.2 and latest samtools mpileup output:
- Tolerate 'Number=R' and new INFO attributes Source and Version
- Tolerate mpileup's '<X>' alt (no alternate allele was observed)
- The 4.3 spec includes '<*>' from gVCF, also meaning no alt al obsvd.
- GT is no longer required; user's example has PL instead, so parse that
into genotypes.
- hgVai now annotates "variants" with <X> and <*> as no_sequence_alteration
- annoFormatVep now uses html encoding for html output in various places so
that "<X>" is displayed properly (custom track labels and various item
names could also have undesirable characters). I am not encoding the
extras' descriptions because those are internal and some have <a>'s.
refs #15625
- src/hg/lib/gpFx.c
- lines changed 25, context: html, text, full: html, text
3640a4d6b3303a6bebc7c5b2fc5abcf7f4fae0b2 Wed Sep 28 11:56:00 2016 -0700
Partial support for changes in VCF4.2 and latest samtools mpileup output:
- Tolerate 'Number=R' and new INFO attributes Source and Version
- Tolerate mpileup's '<X>' alt (no alternate allele was observed)
- The 4.3 spec includes '<*>' from gVCF, also meaning no alt al obsvd.
- GT is no longer required; user's example has PL instead, so parse that
into genotypes.
- hgVai now annotates "variants" with <X> and <*> as no_sequence_alteration
- annoFormatVep now uses html encoding for html output in various places so
that "<X>" is displayed properly (custom track labels and various item
names could also have undesirable characters). I am not encoding the
extras' descriptions because those are internal and some have <a>'s.
refs #15625
- src/hg/lib/hgFind.c
- lines changed 11, context: html, text, full: html, text
a1c329068ad18aa4093972b501e6324f8bcdb398 Fri Sep 16 17:19:30 2016 -0700
Parse HGVS position ranges and coding terms' UTR and intron coordinates.
When the chromAlias table is present, this also now supports NC_*:g. terms.
The sequence change part is no longer parsed -- it's not necessary for mapping
to genomic ranges, although it will be necessary in order for hgVai to take
HGVS input.
This does not yet support ranges-of-ranges but neither does Mutalyzer. This
also doesn't support uncertain positions ('?'). Like complex sequence changes,
those can wait until we have a sophisticated parser.
We also support some new not-quite-HGVS forms: geneSymbol and protein pos only,
or geneSymbol and c.<valid position range>.
refs #15071
- src/hg/lib/hgHgvs.c
- lines changed 794, context: html, text, full: html, text
a1c329068ad18aa4093972b501e6324f8bcdb398 Fri Sep 16 17:19:30 2016 -0700
Parse HGVS position ranges and coding terms' UTR and intron coordinates.
When the chromAlias table is present, this also now supports NC_*:g. terms.
The sequence change part is no longer parsed -- it's not necessary for mapping
to genomic ranges, although it will be necessary in order for hgVai to take
HGVS input.
This does not yet support ranges-of-ranges but neither does Mutalyzer. This
also doesn't support uncertain positions ('?'). Like complex sequence changes,
those can wait until we have a sophisticated parser.
We also support some new not-quite-HGVS forms: geneSymbol and protein pos only,
or geneSymbol and c.<valid position range>.
refs #15071
- lines changed 389, context: html, text, full: html, text
43db133d50ad5cd505cc1ea853b701b271054e91 Mon Sep 26 16:56:04 2016 -0700
Added support for HGVS-like syntax that b0b got from a user: no '.' and NM_ accession with protein change description. Also, if the new ncbiRefSeq* tables are present, use those instead of refSeqAli and Genbank metadata tables.
At this point, ncbiRefSeqPsl is missing some transcripts that are present in other ncbiRefSeq* tables, so if an accession is not found there, try again in refSeqAli and Genbank.
refs #15071, #13673 note-443
- src/hg/lib/jWestBanner.html
- lines changed 1, context: html, text, full: html, text
eaef2d170ea8b272234e9b3bf453cfccf98a5ba0 Fri Sep 30 11:25:40 2016 -0700
Fixing needed encoding of pipe char in URL. refs #18077.
- lines changed 1, context: html, text, full: html, text
f349b0993cebf6c035910b211f8e300901881ef9 Fri Sep 30 11:49:15 2016 -0700
Fixing needed encoding of pipe char in URL. Oops jWestBanner.html must have manually created double %% encoding. refs #18077.
- lines changed 1, context: html, text, full: html, text
2e2953ca15534bf34e976f0da2f3f9aee11b7393 Fri Sep 30 12:46:45 2016 -0700
Fixing needed encoding of pipe colon comma chars in URL. refs #18077.
- src/hg/lib/ncbiRefSeqLink.as
- lines changed 1, context: html, text, full: html, text
dfdffa57a180281078f1158f56d01a78e82bc3f9 Tue Sep 27 10:09:55 2016 -0700
note field is actually a longblob not varchar refs #13673
- src/hg/lib/ncbiRefSeqLink.sql
- lines changed 4, context: html, text, full: html, text
a096f41962e1fec8b70904bcef41eb5f1d40a922 Mon Sep 26 16:35:17 2016 -0700
Adding indexes to ncbiRefSeqLink.sql to speed up queries on fields other than id. refs #13673 note-442
- lines changed 1, context: html, text, full: html, text
dfdffa57a180281078f1158f56d01a78e82bc3f9 Tue Sep 27 10:09:55 2016 -0700
note field is actually a longblob not varchar refs #13673
- src/hg/lib/pgSnp.c
- lines changed 4, context: html, text, full: html, text
3640a4d6b3303a6bebc7c5b2fc5abcf7f4fae0b2 Wed Sep 28 11:56:00 2016 -0700
Partial support for changes in VCF4.2 and latest samtools mpileup output:
- Tolerate 'Number=R' and new INFO attributes Source and Version
- Tolerate mpileup's '<X>' alt (no alternate allele was observed)
- The 4.3 spec includes '<*>' from gVCF, also meaning no alt al obsvd.
- GT is no longer required; user's example has PL instead, so parse that
into genotypes.
- hgVai now annotates "variants" with <X> and <*> as no_sequence_alteration
- annoFormatVep now uses html encoding for html output in various places so
that "<X>" is displayed properly (custom track labels and various item
names could also have undesirable characters). I am not encoding the
extras' descriptions because those are internal and some have <a>'s.
refs #15625
- src/hg/lib/soTerm.c
- lines changed 1, context: html, text, full: html, text
3640a4d6b3303a6bebc7c5b2fc5abcf7f4fae0b2 Wed Sep 28 11:56:00 2016 -0700
Partial support for changes in VCF4.2 and latest samtools mpileup output:
- Tolerate 'Number=R' and new INFO attributes Source and Version
- Tolerate mpileup's '<X>' alt (no alternate allele was observed)
- The 4.3 spec includes '<*>' from gVCF, also meaning no alt al obsvd.
- GT is no longer required; user's example has PL instead, so parse that
into genotypes.
- hgVai now annotates "variants" with <X> and <*> as no_sequence_alteration
- annoFormatVep now uses html encoding for html output in various places so
that "<X>" is displayed properly (custom track labels and various item
names could also have undesirable characters). I am not encoding the
extras' descriptions because those are internal and some have <a>'s.
refs #15625
- src/hg/lib/tests/expected/hgvs/clinVarHgvs.txt
- lines changed 79, context: html, text, full: html, text
a1c329068ad18aa4093972b501e6324f8bcdb398 Fri Sep 16 17:19:30 2016 -0700
Parse HGVS position ranges and coding terms' UTR and intron coordinates.
When the chromAlias table is present, this also now supports NC_*:g. terms.
The sequence change part is no longer parsed -- it's not necessary for mapping
to genomic ranges, although it will be necessary in order for hgVai to take
HGVS input.
This does not yet support ranges-of-ranges but neither does Mutalyzer. This
also doesn't support uncertain positions ('?'). Like complex sequence changes,
those can wait until we have a sophisticated parser.
We also support some new not-quite-HGVS forms: geneSymbol and protein pos only,
or geneSymbol and c.<valid position range>.
refs #15071
- src/hg/lib/tests/expected/hgvs/validTerms.txt
- lines changed 17, context: html, text, full: html, text
a1c329068ad18aa4093972b501e6324f8bcdb398 Fri Sep 16 17:19:30 2016 -0700
Parse HGVS position ranges and coding terms' UTR and intron coordinates.
When the chromAlias table is present, this also now supports NC_*:g. terms.
The sequence change part is no longer parsed -- it's not necessary for mapping
to genomic ranges, although it will be necessary in order for hgVai to take
HGVS input.
This does not yet support ranges-of-ranges but neither does Mutalyzer. This
also doesn't support uncertain positions ('?'). Like complex sequence changes,
those can wait until we have a sophisticated parser.
We also support some new not-quite-HGVS forms: geneSymbol and protein pos only,
or geneSymbol and c.<valid position range>.
refs #15071
- lines changed 3, context: html, text, full: html, text
43db133d50ad5cd505cc1ea853b701b271054e91 Mon Sep 26 16:56:04 2016 -0700
Added support for HGVS-like syntax that b0b got from a user: no '.' and NM_ accession with protein change description. Also, if the new ncbiRefSeq* tables are present, use those instead of refSeqAli and Genbank metadata tables.
At this point, ncbiRefSeqPsl is missing some transcripts that are present in other ncbiRefSeq* tables, so if an accession is not found there, try again in refSeqAli and Genbank.
refs #15071, #13673 note-443
- src/hg/lib/tests/hgvsTester.c
- lines changed 15, context: html, text, full: html, text
a1c329068ad18aa4093972b501e6324f8bcdb398 Fri Sep 16 17:19:30 2016 -0700
Parse HGVS position ranges and coding terms' UTR and intron coordinates.
When the chromAlias table is present, this also now supports NC_*:g. terms.
The sequence change part is no longer parsed -- it's not necessary for mapping
to genomic ranges, although it will be necessary in order for hgVai to take
HGVS input.
This does not yet support ranges-of-ranges but neither does Mutalyzer. This
also doesn't support uncertain positions ('?'). Like complex sequence changes,
those can wait until we have a sophisticated parser.
We also support some new not-quite-HGVS forms: geneSymbol and protein pos only,
or geneSymbol and c.<valid position range>.
refs #15071
- src/hg/lib/tests/hgvsTests.mk
- lines changed 5, context: html, text, full: html, text
a1c329068ad18aa4093972b501e6324f8bcdb398 Fri Sep 16 17:19:30 2016 -0700
Parse HGVS position ranges and coding terms' UTR and intron coordinates.
When the chromAlias table is present, this also now supports NC_*:g. terms.
The sequence change part is no longer parsed -- it's not necessary for mapping
to genomic ranges, although it will be necessary in order for hgVai to take
HGVS input.
This does not yet support ranges-of-ranges but neither does Mutalyzer. This
also doesn't support uncertain positions ('?'). Like complex sequence changes,
those can wait until we have a sophisticated parser.
We also support some new not-quite-HGVS forms: geneSymbol and protein pos only,
or geneSymbol and c.<valid position range>.
refs #15071
- src/hg/lib/tests/input/hgvs/clinVarHgvs.txt
- lines changed 77, context: html, text, full: html, text
a1c329068ad18aa4093972b501e6324f8bcdb398 Fri Sep 16 17:19:30 2016 -0700
Parse HGVS position ranges and coding terms' UTR and intron coordinates.
When the chromAlias table is present, this also now supports NC_*:g. terms.
The sequence change part is no longer parsed -- it's not necessary for mapping
to genomic ranges, although it will be necessary in order for hgVai to take
HGVS input.
This does not yet support ranges-of-ranges but neither does Mutalyzer. This
also doesn't support uncertain positions ('?'). Like complex sequence changes,
those can wait until we have a sophisticated parser.
We also support some new not-quite-HGVS forms: geneSymbol and protein pos only,
or geneSymbol and c.<valid position range>.
refs #15071
- src/hg/lib/tests/input/hgvs/validTerms.txt
- lines changed 10, context: html, text, full: html, text
a1c329068ad18aa4093972b501e6324f8bcdb398 Fri Sep 16 17:19:30 2016 -0700
Parse HGVS position ranges and coding terms' UTR and intron coordinates.
When the chromAlias table is present, this also now supports NC_*:g. terms.
The sequence change part is no longer parsed -- it's not necessary for mapping
to genomic ranges, although it will be necessary in order for hgVai to take
HGVS input.
This does not yet support ranges-of-ranges but neither does Mutalyzer. This
also doesn't support uncertain positions ('?'). Like complex sequence changes,
those can wait until we have a sophisticated parser.
We also support some new not-quite-HGVS forms: geneSymbol and protein pos only,
or geneSymbol and c.<valid position range>.
refs #15071
- lines changed 3, context: html, text, full: html, text
43db133d50ad5cd505cc1ea853b701b271054e91 Mon Sep 26 16:56:04 2016 -0700
Added support for HGVS-like syntax that b0b got from a user: no '.' and NM_ accession with protein change description. Also, if the new ncbiRefSeq* tables are present, use those instead of refSeqAli and Genbank metadata tables.
At this point, ncbiRefSeqPsl is missing some transcripts that are present in other ncbiRefSeq* tables, so if an accession is not found there, try again in refSeqAli and Genbank.
refs #15071, #13673 note-443
- src/hg/lib/variant.c
- lines changed 3, context: html, text, full: html, text
3640a4d6b3303a6bebc7c5b2fc5abcf7f4fae0b2 Wed Sep 28 11:56:00 2016 -0700
Partial support for changes in VCF4.2 and latest samtools mpileup output:
- Tolerate 'Number=R' and new INFO attributes Source and Version
- Tolerate mpileup's '<X>' alt (no alternate allele was observed)
- The 4.3 spec includes '<*>' from gVCF, also meaning no alt al obsvd.
- GT is no longer required; user's example has PL instead, so parse that
into genotypes.
- hgVai now annotates "variants" with <X> and <*> as no_sequence_alteration
- annoFormatVep now uses html encoding for html output in various places so
that "<X>" is displayed properly (custom track labels and various item
names could also have undesirable characters). I am not encoding the
extras' descriptions because those are internal and some have <a>'s.
refs #15625
- src/hg/makeDb/crisprTrack/README.txt
- lines changed 7, context: html, text, full: html, text
1bd4d2a2296d53ef037a766e3b8f62f9f09e0708 Tue Sep 27 16:14:17 2016 -0700
cleaning up my language in the crispr track readme file
- src/hg/makeDb/crisprTrack/createBigBed.py
- lines changed 3, context: html, text, full: html, text
3bc389356a669e4a57fd41b63e13ad7f424b048d Tue Sep 27 10:22:52 2016 -0700
removing gaps from the processed ranges after feedback from Chris,
refs #17235
- src/hg/makeDb/crisprTrack/doCrispr.sh
- lines changed 3, context: html, text, full: html, text
3bc389356a669e4a57fd41b63e13ad7f424b048d Tue Sep 27 10:22:52 2016 -0700
removing gaps from the processed ranges after feedback from Chris,
refs #17235
- src/hg/makeDb/doc/ce10.txt
- lines changed 1, context: html, text, full: html, text
657e63311ee339a7ed1498d3a62edf9773014de1 Wed Sep 28 14:26:40 2016 -0700
fixing crispr makedoc, refs #71235
- src/hg/makeDb/doc/chlSab2/initialBuild.txt
- lines changed 14, context: html, text, full: html, text
18c9ff3cb02dd9925f4af40e8cb2afa5b8acf1d7 Tue Sep 27 09:09:10 2016 -0700
add augustusGene build procedure refs #11172
- lines changed 12, context: html, text, full: html, text
5e2cd01c4cb69426e70eb896a79b9161e09b458e Tue Sep 27 20:22:07 2016 -0700
added blat server entry refs #11172
- src/hg/makeDb/doc/chlSab2/lastzRuns.txt
- lines changed 27, context: html, text, full: html, text
a0017e089a5709efe65e3d83e6553685efd04c5b Wed Sep 28 09:40:20 2016 -0700
lastz run rheMac8<->chlSab2 refs #11172
- src/hg/makeDb/doc/ci2.txt
- lines changed 1, context: html, text, full: html, text
657e63311ee339a7ed1498d3a62edf9773014de1 Wed Sep 28 14:26:40 2016 -0700
fixing crispr makedoc, refs #71235
- src/hg/makeDb/doc/danRer7.txt
- lines changed 1, context: html, text, full: html, text
657e63311ee339a7ed1498d3a62edf9773014de1 Wed Sep 28 14:26:40 2016 -0700
fixing crispr makedoc, refs #71235
- src/hg/makeDb/doc/dm6.txt
- lines changed 5, context: html, text, full: html, text
7ac8a6d873de1fdbe7f7373cf2dc97e7b094eef5 Mon Sep 26 17:54:12 2016 -0700
repair pfam tracks
- lines changed 1, context: html, text, full: html, text
657e63311ee339a7ed1498d3a62edf9773014de1 Wed Sep 28 14:26:40 2016 -0700
fixing crispr makedoc, refs #71235
- src/hg/makeDb/doc/hg19.txt
- lines changed 1, context: html, text, full: html, text
657e63311ee339a7ed1498d3a62edf9773014de1 Wed Sep 28 14:26:40 2016 -0700
fixing crispr makedoc, refs #71235
- lines changed 1, context: html, text, full: html, text
fc8e1c340b7b97b65b0855e7ef4b092f35d498c8 Wed Sep 28 14:50:20 2016 -0700
fixing hg19 crispr makedoc, refs #17235
- src/hg/makeDb/doc/hg38/crispr.txt
- lines changed 1, context: html, text, full: html, text
657e63311ee339a7ed1498d3a62edf9773014de1 Wed Sep 28 14:26:40 2016 -0700
fixing crispr makedoc, refs #71235
- src/hg/makeDb/doc/hg38/lastzRuns.txt
- lines changed 70, context: html, text, full: html, text
50e969e34bee10a3079893be39eb44df3e4ad13b Wed Sep 28 11:38:16 2016 -0700
add hg38<->chlSab2 procedure refs #11172
- src/hg/makeDb/doc/hg38/multiz100way.txt
- lines changed 8, context: html, text, full: html, text
7b89c304567373d9f309086a965706dcaa2a7670 Wed Sep 28 15:49:42 2016 -0700
if there is a maf with just the default species, use that instead of the
main maf
- src/hg/makeDb/doc/mm10.txt
- lines changed 1, context: html, text, full: html, text
657e63311ee339a7ed1498d3a62edf9773014de1 Wed Sep 28 14:26:40 2016 -0700
fixing crispr makedoc, refs #71235
- src/hg/makeDb/doc/rheMac8/lastzRuns.txt
- lines changed 73, context: html, text, full: html, text
a0017e089a5709efe65e3d83e6553685efd04c5b Wed Sep 28 09:40:20 2016 -0700
lastz run rheMac8<->chlSab2 refs #11172
- src/hg/makeDb/doc/rn5.txt
- lines changed 1, context: html, text, full: html, text
657e63311ee339a7ed1498d3a62edf9773014de1 Wed Sep 28 14:26:40 2016 -0700
fixing crispr makedoc, refs #71235
- src/hg/makeDb/doc/sacCer3.txt
- lines changed 1, context: html, text, full: html, text
657e63311ee339a7ed1498d3a62edf9773014de1 Wed Sep 28 14:26:40 2016 -0700
fixing crispr makedoc, refs #71235
- src/hg/makeDb/doc/ucscGenes/hg18.ucscGenes11.csh
- lines changed 2, context: html, text, full: html, text
7ac8a6d873de1fdbe7f7373cf2dc97e7b094eef5 Mon Sep 26 17:54:12 2016 -0700
repair pfam tracks
- src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes14.csh
- lines changed 2, context: html, text, full: html, text
7ac8a6d873de1fdbe7f7373cf2dc97e7b094eef5 Mon Sep 26 17:54:12 2016 -0700
repair pfam tracks
- src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes17.sh
- lines changed 1, context: html, text, full: html, text
7ac8a6d873de1fdbe7f7373cf2dc97e7b094eef5 Mon Sep 26 17:54:12 2016 -0700
repair pfam tracks
- src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes16.csh
- lines changed 2, context: html, text, full: html, text
7ac8a6d873de1fdbe7f7373cf2dc97e7b094eef5 Mon Sep 26 17:54:12 2016 -0700
repair pfam tracks
- src/hg/makeDb/doc/ucscGenes/mm9.ucscGenes12.csh
- lines changed 2, context: html, text, full: html, text
7ac8a6d873de1fdbe7f7373cf2dc97e7b094eef5 Mon Sep 26 17:54:12 2016 -0700
repair pfam tracks
- src/hg/makeDb/trackDb/chimp/panTro5/description.html
- lines changed 2, context: html, text, full: html, text
d11f472d623b7efa4ef625628becfcb55ff45d4e Mon Sep 26 12:44:07 2016 -0700
update pantro5 Gateway page
- src/hg/makeDb/trackDb/chimp/panTro5/trackDb.chainNet.ra
- lines changed 5, context: html, text, full: html, text
cad5013c2729c5d804347df274475334dca119ea Tue Sep 27 13:40:38 2016 -0700
fixing up chain net description pages
- src/hg/makeDb/trackDb/chimp/panTro5/trackDb.ra
- lines changed 5, context: html, text, full: html, text
fd84290ec8d76b0af18a5ac54e6c921369ddad01 Tue Sep 27 10:15:48 2016 -0700
add gold track search rule refs #17817
- lines changed 2, context: html, text, full: html, text
cad5013c2729c5d804347df274475334dca119ea Tue Sep 27 13:40:38 2016 -0700
fixing up chain net description pages
- lines changed 8, context: html, text, full: html, text
4b7925b419c8aa1cc7eb5ff8afef5b1dda2ae3f8 Tue Sep 27 13:44:04 2016 -0700
fixing merge conflict
- src/hg/makeDb/trackDb/chlorocebus/chlSab2/trackDb.chainNet.ra
- lines changed 10, context: html, text, full: html, text
5610b82206f1ffd14c925bab4fbf92ec5db68fbe Tue Sep 27 16:27:50 2016 -0700
Fixing chain description pages, refs #11172
- lines changed 6, context: html, text, full: html, text
6f456d23ec5b86a028047eac7dce32ce1e191dbd Wed Sep 28 11:57:00 2016 -0700
Fixing up parameters on chainNetRheMac8 description page, refs #11172
- src/hg/makeDb/trackDb/chlorocebus/chlSab2/trackDb.ra
- lines changed 6, context: html, text, full: html, text
fec600e05daccff1cad623a4141e10c627f3fb20 Tue Sep 27 11:12:45 2016 -0700
Fixing minor typo on crispr description page and changing default track viz for chlSab2
- lines changed 5, context: html, text, full: html, text
5610b82206f1ffd14c925bab4fbf92ec5db68fbe Tue Sep 27 16:27:50 2016 -0700
Fixing chain description pages, refs #11172
- src/hg/makeDb/trackDb/crispr.html
- lines changed 2, context: html, text, full: html, text
fec600e05daccff1cad623a4141e10c627f3fb20 Tue Sep 27 11:12:45 2016 -0700
Fixing minor typo on crispr description page and changing default track viz for chlSab2
- lines changed 6, context: html, text, full: html, text
f5c78f0711ba4356d4311e01f61c8b3d247c89cb Fri Sep 30 09:03:14 2016 -0700
Some minor changes to crispr track description page and including description page on each subtrack, refs #17235
- lines changed 1, context: html, text, full: html, text
3a5516d5db87e024ad8793be8899784627761001 Fri Sep 30 11:53:36 2016 -0700
Adding hg19 and hg38 specific crispr pages and generalizing top level description page, refs #17235
- src/hg/makeDb/trackDb/ebola/eboVir3/cons160way.html
- lines changed 8, context: html, text, full: html, text
51545628ac45d27546597aa684d0dc529a236f16 Fri Sep 30 16:38:34 2016 -0700
made refernce to the colors in COLOR on html page
- lines changed 1, context: html, text, full: html, text
e7182cbd3c395428fb48bfe0e4662b97fc29a8c7 Fri Sep 30 16:44:50 2016 -0700
fixed egregious grammar nit
- src/hg/makeDb/trackDb/ebola/eboVir3/description.html
- lines changed 5, context: html, text, full: html, text
e06f0b8c8055093e52aadfe195d539bcb3bda74f Wed Sep 28 09:01:05 2016 -0700
Added link to downloads from Ebola portal page. Added link to portal from ebola gateway description page. refs #18149
- src/hg/makeDb/trackDb/gorilla/gorGor5/trackDb.chainNet.ra
- lines changed 11, context: html, text, full: html, text
6c9423b7a9c39de7784bb178ba2f0253a0338cb0 Tue Sep 27 13:54:12 2016 -0700
Fixing chain/net track description pages, refs #17580
- src/hg/makeDb/trackDb/gorilla/gorGor5/trackDb.ra
- lines changed 6, context: html, text, full: html, text
a2dea7a11090f6d5eb772119af060129fdcbd263 Tue Sep 27 10:13:46 2016 -0700
add gold track search rule refs #17580
- lines changed 1, context: html, text, full: html, text
6c9423b7a9c39de7784bb178ba2f0253a0338cb0 Tue Sep 27 13:54:12 2016 -0700
Fixing chain/net track description pages, refs #17580
- lines changed 1, context: html, text, full: html, text
fac70fc837a878f031d2583b3e88bae1cf9c503a Tue Sep 27 13:57:35 2016 -0700
Fixing include stanza, refs #17580
- src/hg/makeDb/trackDb/human/hg18/omimAvSnp.html
- lines changed 5, context: html, text, full: html, text
b3d9ffbeccccf63450526eb5f4b55de65ab3c753 Fri Sep 30 11:27:53 2016 -0700
changing text in html file to reflect change in OMIM track names. refs #18136, #17831
- src/hg/makeDb/trackDb/human/hg18/trackDb.ra
- lines changed 1, context: html, text, full: html, text
19d83147960677bdfda960efe6102a865c34b314 Tue Sep 27 13:24:33 2016 -0700
Putting hg19 NumtS track in Repeats group, moving hg18 chainSelf to Variation + Repeats group, refs #18083
- src/hg/makeDb/trackDb/human/hg19/crispr.html
- lines changed 162, context: html, text, full: html, text
3a5516d5db87e024ad8793be8899784627761001 Fri Sep 30 11:53:36 2016 -0700
Adding hg19 and hg38 specific crispr pages and generalizing top level description page, refs #17235
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 1, context: html, text, full: html, text
19d83147960677bdfda960efe6102a865c34b314 Tue Sep 27 13:24:33 2016 -0700
Putting hg19 NumtS track in Repeats group, moving hg18 chainSelf to Variation + Repeats group, refs #18083
- lines changed 4, context: html, text, full: html, text
3a5516d5db87e024ad8793be8899784627761001 Fri Sep 30 11:53:36 2016 -0700
Adding hg19 and hg38 specific crispr pages and generalizing top level description page, refs #17235
- src/hg/makeDb/trackDb/human/hg38/crispr.html
- lines changed 162, context: html, text, full: html, text
3a5516d5db87e024ad8793be8899784627761001 Fri Sep 30 11:53:36 2016 -0700
Adding hg19 and hg38 specific crispr pages and generalizing top level description page, refs #17235
- lines changed 43, context: html, text, full: html, text
b660d9e37ed7562c12870acd6fb8c1765fdc64a2 Fri Sep 30 15:00:47 2016 -0700
Alphabetizing references and minor changes to format, refs #17235
- src/hg/makeDb/trackDb/human/hg38/omimDescriptionText.html
- lines changed 1, context: html, text, full: html, text
b3d9ffbeccccf63450526eb5f4b55de65ab3c753 Fri Sep 30 11:27:53 2016 -0700
changing text in html file to reflect change in OMIM track names. refs #18136, #17831
- src/hg/makeDb/trackDb/human/hg38/trackDb.100way.ra
- lines changed 2, context: html, text, full: html, text
7b89c304567373d9f309086a965706dcaa2a7670 Wed Sep 28 15:49:42 2016 -0700
if there is a maf with just the default species, use that instead of the
main maf
- src/hg/makeDb/trackDb/human/hg38/trackDb.ra
- lines changed 4, context: html, text, full: html, text
3a5516d5db87e024ad8793be8899784627761001 Fri Sep 30 11:53:36 2016 -0700
Adding hg19 and hg38 specific crispr pages and generalizing top level description page, refs #17235
- src/hg/makeDb/trackDb/human/omimAvSnp.html
- lines changed 3, context: html, text, full: html, text
b3d9ffbeccccf63450526eb5f4b55de65ab3c753 Fri Sep 30 11:27:53 2016 -0700
changing text in html file to reflect change in OMIM track names. refs #18136, #17831
- src/hg/makeDb/trackDb/human/omimDescriptionText.html
- lines changed 1, context: html, text, full: html, text
b3d9ffbeccccf63450526eb5f4b55de65ab3c753 Fri Sep 30 11:27:53 2016 -0700
changing text in html file to reflect change in OMIM track names. refs #18136, #17831
- src/hg/makeDb/trackDb/tagTypes.tab
- lines changed 2, context: html, text, full: html, text
7b89c304567373d9f309086a965706dcaa2a7670 Wed Sep 28 15:49:42 2016 -0700
if there is a maf with just the default species, use that instead of the
main maf
- src/hg/makeDb/trackDb/trackDb.ra
- lines changed 3, context: html, text, full: html, text
f5c78f0711ba4356d4311e01f61c8b3d247c89cb Fri Sep 30 09:03:14 2016 -0700
Some minor changes to crispr track description page and including description page on each subtrack, refs #17235
- lines changed 14, context: html, text, full: html, text
b8ca58b9e58db93eb210de2edf5b36e773f1a163 Fri Sep 30 11:22:09 2016 -0700
Updating some long and short labels for NCBI RefSeq track, refs #13673
- src/inc/dnautil.h
- lines changed 4, context: html, text, full: html, text
a1c329068ad18aa4093972b501e6324f8bcdb398 Fri Sep 16 17:19:30 2016 -0700
Parse HGVS position ranges and coding terms' UTR and intron coordinates.
When the chromAlias table is present, this also now supports NC_*:g. terms.
The sequence change part is no longer parsed -- it's not necessary for mapping
to genomic ranges, although it will be necessary in order for hgVai to take
HGVS input.
This does not yet support ranges-of-ranges but neither does Mutalyzer. This
also doesn't support uncertain positions ('?'). Like complex sequence changes,
those can wait until we have a sophisticated parser.
We also support some new not-quite-HGVS forms: geneSymbol and protein pos only,
or geneSymbol and c.<valid position range>.
refs #15071
- src/inc/htmshell.h
- lines changed 12, context: html, text, full: html, text
ea3a67989847a2b731be271d112feab992a5eb9a Wed Sep 28 10:08:47 2016 -0700
Fixes hgNearTest robot by having htmlPage.c call attributeDecode on attribute values since we are now encoding them against XSS. refs #18077. hgNearTest was crashing right away with the error Couldn't get main form on orgPage.
- src/lib/cheapcgi.c
- lines changed 2, context: html, text, full: html, text
ea3a67989847a2b731be271d112feab992a5eb9a Wed Sep 28 10:08:47 2016 -0700
Fixes hgNearTest robot by having htmlPage.c call attributeDecode on attribute values since we are now encoding them against XSS. refs #18077. hgNearTest was crashing right away with the error Couldn't get main form on orgPage.
- src/lib/dnautil.c
- lines changed 16, context: html, text, full: html, text
a1c329068ad18aa4093972b501e6324f8bcdb398 Fri Sep 16 17:19:30 2016 -0700
Parse HGVS position ranges and coding terms' UTR and intron coordinates.
When the chromAlias table is present, this also now supports NC_*:g. terms.
The sequence change part is no longer parsed -- it's not necessary for mapping
to genomic ranges, although it will be necessary in order for hgVai to take
HGVS input.
This does not yet support ranges-of-ranges but neither does Mutalyzer. This
also doesn't support uncertain positions ('?'). Like complex sequence changes,
those can wait until we have a sophisticated parser.
We also support some new not-quite-HGVS forms: geneSymbol and protein pos only,
or geneSymbol and c.<valid position range>.
refs #15071
- src/lib/htmlPage.c
- lines changed 2, context: html, text, full: html, text
ea3a67989847a2b731be271d112feab992a5eb9a Wed Sep 28 10:08:47 2016 -0700
Fixes hgNearTest robot by having htmlPage.c call attributeDecode on attribute values since we are now encoding them against XSS. refs #18077. hgNearTest was crashing right away with the error Couldn't get main form on orgPage.
- src/lib/htmshell.c
- lines changed 145, context: html, text, full: html, text
ea3a67989847a2b731be271d112feab992a5eb9a Wed Sep 28 10:08:47 2016 -0700
Fixes hgNearTest robot by having htmlPage.c call attributeDecode on attribute values since we are now encoding them against XSS. refs #18077. hgNearTest was crashing right away with the error Couldn't get main form on orgPage.
- lines changed 4, context: html, text, full: html, text
817a4491709c2168643fab6b3fc342531dcbbec9 Fri Sep 30 13:47:59 2016 -0700
Fixes Very Early Warning html handler to encode printf parameters. Fixes #18162.
- lines changed 1, context: html, text, full: html, text
f8b7740e1898ae4a2ad289ef043a541c4179e0ae Fri Sep 30 12:05:55 2016 -0700
Expand vaHtmlSafefNoAbort's newFormatSize 3x instead of 2x to prevent uncaught overflow on format strings composed mostly of %s's, since 3 bytes are added for every %s (two bytes expand to five bytes).
- src/lib/tests/makefile
- lines changed 7, context: html, text, full: html, text
ea3a67989847a2b731be271d112feab992a5eb9a Wed Sep 28 10:08:47 2016 -0700
Fixes hgNearTest robot by having htmlPage.c call attributeDecode on attribute values since we are now encoding them against XSS. refs #18077. hgNearTest was crashing right away with the error Couldn't get main form on orgPage.
- src/lib/tests/testDecodedString.c
- lines changed 77, context: html, text, full: html, text
ea3a67989847a2b731be271d112feab992a5eb9a Wed Sep 28 10:08:47 2016 -0700
Fixes hgNearTest robot by having htmlPage.c call attributeDecode on attribute values since we are now encoding them against XSS. refs #18077. hgNearTest was crashing right away with the error Couldn't get main form on orgPage.
- src/lib/vcf.c
- lines changed 112, context: html, text, full: html, text
3640a4d6b3303a6bebc7c5b2fc5abcf7f4fae0b2 Wed Sep 28 11:56:00 2016 -0700
Partial support for changes in VCF4.2 and latest samtools mpileup output:
- Tolerate 'Number=R' and new INFO attributes Source and Version
- Tolerate mpileup's '<X>' alt (no alternate allele was observed)
- The 4.3 spec includes '<*>' from gVCF, also meaning no alt al obsvd.
- GT is no longer required; user's example has PL instead, so parse that
into genotypes.
- hgVai now annotates "variants" with <X> and <*> as no_sequence_alteration
- annoFormatVep now uses html encoding for html output in various places so
that "<X>" is displayed properly (custom track labels and various item
names could also have undesirable characters). I am not encoding the
extras' descriptions because those are internal and some have <a>'s.
refs #15625
- src/utils/doLocusName
- lines changed 13, context: html, text, full: html, text
9b8c6b6168c9f5a70ef7270a78bd2536bb2ce8b6 Fri Sep 30 01:25:57 2016 -0700
allow doLocusName to work with knowGene, refs #17235
- src/utils/qa/bigPush.sh
- lines changed 2, context: html, text, full: html, text
f5b67179ac3ebd77c8d502585f1463214fed208a Tue Sep 27 14:13:41 2016 -0700
Minor correction to usage statement for bigPush script to reflect current behavior of -v option, no redmine
- src/utils/qa/countPerChrom.csh
- lines changed 1, context: html, text, full: html, text
4a2e4209dd33c8e627c179264b266ca25a76a4fa Wed Sep 28 13:06:04 2016 -0700
Adding alts to list of things we ignore in histogram mode, refs #17987
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed 2, context: html, text, full: html, text
cace572da12cdfc6c4d44cedd17a0ca864294475 Mon Oct 3 10:34:50 2016 -0700
v340 preview1
- src/utils/qa/weeklybld/doHgNearTestRobot.csh
- lines changed 2, context: html, text, full: html, text
29c0f39aee9874a3d0688ccf35a7f33657eeb598 Mon Sep 26 20:30:44 2016 -0700
fixup broken mail command refs #17782
- src/utils/qa/weeklybld/revertCommits.csh
- lines changed 1, context: html, text, full: html, text
7ce2eedf2b207cf4f95cf1a7bd1dbb83e8b49042 Wed Sep 28 15:40:06 2016 -0700
now working on hgwdev instead of hgwbeta refs #18152
- lines changed: 2909
- files changed: 119
