All File Changes
v292_base to v293_preview (2013-11-11 to 2013-11-18) v293
- src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwUser/makefile
- lines changed 17, context: html, text, full: html, text
Add oneShot/rsyncEdwUser directory and rsyncEdwUser.c for resync user table from endcodedcc.
- src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwUser/rsyncEdwUser.c
- lines changed 79, context: html, text, full: html, text
Add oneShot/rsyncEdwUser directory and rsyncEdwUser.c for resync user table from endcodedcc.
- src/hg/encode3/validateManifest/VERSION.TXT
- lines changed 2, context: html, text, full: html, text
little update vm version.txt
- src/hg/encode3/validateManifest/validateManifest.c
- lines changed 7, context: html, text, full: html, text
check specifically for a blank format
- lines changed 1, context: html, text, full: html, text
improve err mesg vm for bad format/compression combos.
- src/hg/genePredToFakePsl/genePredToFakePsl.c
- lines changed 32, context: html, text, full: html, text
Two new tracks for Locus Reference Genomic (LRG) (#11863) with customhandlers: LRG Regions and LRG Transcripts.
LRGs are frozen reference sequences for a particular gene plus some
upstream and downstream sequence. They are intended to provide a
stable coordinate system for gene annotations that won't change
with every new genome assembly, but can be mapped to each genome
assembly. Since there is a lot of metadata associated with each
region, I made LRG Regions a bigBed 12 + with fields describing
mismatches and indels, so that PSL can be derived from the bigBed
and the original LRG sequence can be reconstructed using genome
assembly sequence and the mismatch/indel info. hgTracks shows
differences and LRG insertions into the reference assembly using
the cds.c baseColor code. (LRG deletions from the reference appear
as gaps, which we get for free with bed12 info).
For LRG Transcripts, I found the genePred codon-coloring code
inadequate for showing an insertion into hg19 (or even mismatches),
so instead of genePred I ended up using PSL + sequence, more like
the mRNA track representation and display.
- src/hg/hgTrackUi/hgTrackUi.c
- lines changed 4, context: html, text, full: html, text
Two new tracks for Locus Reference Genomic (LRG) (#11863) with customhandlers: LRG Regions and LRG Transcripts.
LRGs are frozen reference sequences for a particular gene plus some
upstream and downstream sequence. They are intended to provide a
stable coordinate system for gene annotations that won't change
with every new genome assembly, but can be mapped to each genome
assembly. Since there is a lot of metadata associated with each
region, I made LRG Regions a bigBed 12 + with fields describing
mismatches and indels, so that PSL can be derived from the bigBed
and the original LRG sequence can be reconstructed using genome
assembly sequence and the mismatch/indel info. hgTracks shows
differences and LRG insertions into the reference assembly using
the cds.c baseColor code. (LRG deletions from the reference appear
as gaps, which we get for free with bed12 info).
For LRG Transcripts, I found the genePred codon-coloring code
inadequate for showing an insertion into hg19 (or even mismatches),
so instead of genePred I ended up using PSL + sequence, more like
the mRNA track representation and display.
- src/hg/hgTracks/cds.c
- lines changed 26, context: html, text, full: html, text
Two new tracks for Locus Reference Genomic (LRG) (#11863) with customhandlers: LRG Regions and LRG Transcripts.
LRGs are frozen reference sequences for a particular gene plus some
upstream and downstream sequence. They are intended to provide a
stable coordinate system for gene annotations that won't change
with every new genome assembly, but can be mapped to each genome
assembly. Since there is a lot of metadata associated with each
region, I made LRG Regions a bigBed 12 + with fields describing
mismatches and indels, so that PSL can be derived from the bigBed
and the original LRG sequence can be reconstructed using genome
assembly sequence and the mismatch/indel info. hgTracks shows
differences and LRG insertions into the reference assembly using
the cds.c baseColor code. (LRG deletions from the reference appear
as gaps, which we get for free with bed12 info).
For LRG Transcripts, I found the genePred codon-coloring code
inadequate for showing an insertion into hg19 (or even mismatches),
so instead of genePred I ended up using PSL + sequence, more like
the mRNA track representation and display.
- src/hg/hgTracks/hgTracks.h
- lines changed 3, context: html, text, full: html, text
Two new tracks for Locus Reference Genomic (LRG) (#11863) with customhandlers: LRG Regions and LRG Transcripts.
LRGs are frozen reference sequences for a particular gene plus some
upstream and downstream sequence. They are intended to provide a
stable coordinate system for gene annotations that won't change
with every new genome assembly, but can be mapped to each genome
assembly. Since there is a lot of metadata associated with each
region, I made LRG Regions a bigBed 12 + with fields describing
mismatches and indels, so that PSL can be derived from the bigBed
and the original LRG sequence can be reconstructed using genome
assembly sequence and the mismatch/indel info. hgTracks shows
differences and LRG insertions into the reference assembly using
the cds.c baseColor code. (LRG deletions from the reference appear
as gaps, which we get for free with bed12 info).
For LRG Transcripts, I found the genePred codon-coloring code
inadequate for showing an insertion into hg19 (or even mismatches),
so instead of genePred I ended up using PSL + sequence, more like
the mRNA track representation and display.
- src/hg/hgTracks/lrgTrack.c
- lines changed 62, context: html, text, full: html, text
Two new tracks for Locus Reference Genomic (LRG) (#11863) with customhandlers: LRG Regions and LRG Transcripts.
LRGs are frozen reference sequences for a particular gene plus some
upstream and downstream sequence. They are intended to provide a
stable coordinate system for gene annotations that won't change
with every new genome assembly, but can be mapped to each genome
assembly. Since there is a lot of metadata associated with each
region, I made LRG Regions a bigBed 12 + with fields describing
mismatches and indels, so that PSL can be derived from the bigBed
and the original LRG sequence can be reconstructed using genome
assembly sequence and the mismatch/indel info. hgTracks shows
differences and LRG insertions into the reference assembly using
the cds.c baseColor code. (LRG deletions from the reference appear
as gaps, which we get for free with bed12 info).
For LRG Transcripts, I found the genePred codon-coloring code
inadequate for showing an insertion into hg19 (or even mismatches),
so instead of genePred I ended up using PSL + sequence, more like
the mRNA track representation and display.
- src/hg/hgTracks/makefile
- lines changed 4, context: html, text, full: html, text
Two new tracks for Locus Reference Genomic (LRG) (#11863) with customhandlers: LRG Regions and LRG Transcripts.
LRGs are frozen reference sequences for a particular gene plus some
upstream and downstream sequence. They are intended to provide a
stable coordinate system for gene annotations that won't change
with every new genome assembly, but can be mapped to each genome
assembly. Since there is a lot of metadata associated with each
region, I made LRG Regions a bigBed 12 + with fields describing
mismatches and indels, so that PSL can be derived from the bigBed
and the original LRG sequence can be reconstructed using genome
assembly sequence and the mismatch/indel info. hgTracks shows
differences and LRG insertions into the reference assembly using
the cds.c baseColor code. (LRG deletions from the reference appear
as gaps, which we get for free with bed12 info).
For LRG Transcripts, I found the genePred codon-coloring code
inadequate for showing an insertion into hg19 (or even mismatches),
so instead of genePred I ended up using PSL + sequence, more like
the mRNA track representation and display.
- src/hg/hgTracks/simpleTracks.c
- lines changed 2, context: html, text, full: html, text
Two new tracks for Locus Reference Genomic (LRG) (#11863) with customhandlers: LRG Regions and LRG Transcripts.
LRGs are frozen reference sequences for a particular gene plus some
upstream and downstream sequence. They are intended to provide a
stable coordinate system for gene annotations that won't change
with every new genome assembly, but can be mapped to each genome
assembly. Since there is a lot of metadata associated with each
region, I made LRG Regions a bigBed 12 + with fields describing
mismatches and indels, so that PSL can be derived from the bigBed
and the original LRG sequence can be reconstructed using genome
assembly sequence and the mismatch/indel info. hgTracks shows
differences and LRG insertions into the reference assembly using
the cds.c baseColor code. (LRG deletions from the reference appear
as gaps, which we get for free with bed12 info).
For LRG Transcripts, I found the genePred codon-coloring code
inadequate for showing an insertion into hg19 (or even mismatches),
so instead of genePred I ended up using PSL + sequence, more like
the mRNA track representation and display.
- src/hg/hgVai/hgVai.c
- lines changed 394, context: html, text, full: html, text
Work in progress for #11460 (paste/upload variant input options...):adding an option for user to paste/upload variant identifiers which
will be translated into a sorted list of vcfRecords.
Currently we recognize only rs# IDs. I was considering adding
dbVar IDs, but those could come from multiple sources (DGV, ClinVar,
ISCA) so I'm not sure.
Treating all symbolic/named alleles as deletions... non-ideal,
but fortunately those are a small minority in dbSNP.
Next: recognize HGVS IDs.
The grander vision of #11460 includes accepting VEP input format
and VCF, but I think those should be new SELECT options so we don't
get into quagmire of guessing format.
- src/hg/hgc/hgc.c
- lines changed 108, context: html, text, full: html, text
Two new tracks for Locus Reference Genomic (LRG) (#11863) with customhandlers: LRG Regions and LRG Transcripts.
LRGs are frozen reference sequences for a particular gene plus some
upstream and downstream sequence. They are intended to provide a
stable coordinate system for gene annotations that won't change
with every new genome assembly, but can be mapped to each genome
assembly. Since there is a lot of metadata associated with each
region, I made LRG Regions a bigBed 12 + with fields describing
mismatches and indels, so that PSL can be derived from the bigBed
and the original LRG sequence can be reconstructed using genome
assembly sequence and the mismatch/indel info. hgTracks shows
differences and LRG insertions into the reference assembly using
the cds.c baseColor code. (LRG deletions from the reference appear
as gaps, which we get for free with bed12 info).
For LRG Transcripts, I found the genePred codon-coloring code
inadequate for showing an insertion into hg19 (or even mismatches),
so instead of genePred I ended up using PSL + sequence, more like
the mRNA track representation and display.
- src/hg/hgc/hgc.h
- lines changed 12, context: html, text, full: html, text
Two new tracks for Locus Reference Genomic (LRG) (#11863) with customhandlers: LRG Regions and LRG Transcripts.
LRGs are frozen reference sequences for a particular gene plus some
upstream and downstream sequence. They are intended to provide a
stable coordinate system for gene annotations that won't change
with every new genome assembly, but can be mapped to each genome
assembly. Since there is a lot of metadata associated with each
region, I made LRG Regions a bigBed 12 + with fields describing
mismatches and indels, so that PSL can be derived from the bigBed
and the original LRG sequence can be reconstructed using genome
assembly sequence and the mismatch/indel info. hgTracks shows
differences and LRG insertions into the reference assembly using
the cds.c baseColor code. (LRG deletions from the reference appear
as gaps, which we get for free with bed12 info).
For LRG Transcripts, I found the genePred codon-coloring code
inadequate for showing an insertion into hg19 (or even mismatches),
so instead of genePred I ended up using PSL + sequence, more like
the mRNA track representation and display.
- src/hg/hgc/lrgClick.c
- lines changed 248, context: html, text, full: html, text
Two new tracks for Locus Reference Genomic (LRG) (#11863) with customhandlers: LRG Regions and LRG Transcripts.
LRGs are frozen reference sequences for a particular gene plus some
upstream and downstream sequence. They are intended to provide a
stable coordinate system for gene annotations that won't change
with every new genome assembly, but can be mapped to each genome
assembly. Since there is a lot of metadata associated with each
region, I made LRG Regions a bigBed 12 + with fields describing
mismatches and indels, so that PSL can be derived from the bigBed
and the original LRG sequence can be reconstructed using genome
assembly sequence and the mismatch/indel info. hgTracks shows
differences and LRG insertions into the reference assembly using
the cds.c baseColor code. (LRG deletions from the reference appear
as gaps, which we get for free with bed12 info).
For LRG Transcripts, I found the genePred codon-coloring code
inadequate for showing an insertion into hg19 (or even mismatches),
so instead of genePred I ended up using PSL + sequence, more like
the mRNA track representation and display.
- src/hg/hgc/makefile
- lines changed 2, context: html, text, full: html, text
Two new tracks for Locus Reference Genomic (LRG) (#11863) with customhandlers: LRG Regions and LRG Transcripts.
LRGs are frozen reference sequences for a particular gene plus some
upstream and downstream sequence. They are intended to provide a
stable coordinate system for gene annotations that won't change
with every new genome assembly, but can be mapped to each genome
assembly. Since there is a lot of metadata associated with each
region, I made LRG Regions a bigBed 12 + with fields describing
mismatches and indels, so that PSL can be derived from the bigBed
and the original LRG sequence can be reconstructed using genome
assembly sequence and the mismatch/indel info. hgTracks shows
differences and LRG insertions into the reference assembly using
the cds.c baseColor code. (LRG deletions from the reference appear
as gaps, which we get for free with bed12 info).
For LRG Transcripts, I found the genePred codon-coloring code
inadequate for showing an insertion into hg19 (or even mismatches),
so instead of genePred I ended up using PSL + sequence, more like
the mRNA track representation and display.
- src/hg/htdocs/FAQ/FAQlicense.html
- lines changed 43, context: html, text, full: html, text
Adding FAQ about minimum system requirements for a mirror, refs #11941
- src/hg/htdocs/goldenPath/help/bigWig.html
- lines changed 7, context: html, text, full: html, text
Made changes suggested by Donna in code review (redmine #12134)
- src/hg/htdocs/goldenPath/help/hgTracksHelp.html
- lines changed 3, context: html, text, full: html, text
Changing some limitation numbers in the BLAT help section, refs #11896
- src/hg/htdocs/goldenPath/help/mysql.html
- lines changed 2, context: html, text, full: html, text
Adding central.db=hgcentral line to places where we explain needed .hg.conf refs #12170
- src/hg/htdocs/goldenPath/pubs.html
- lines changed 20, context: html, text, full: html, text
Added Braney track hubs paper (early access -- DOI only) and stub for NAR DB paper (not available online yet). Will update these when they are both in PubMed.
- src/hg/htdocs/mirror.html
- lines changed 16, context: html, text, full: html, text
Adding Australian mirror to our official list of mirrors, refs #12092
- src/hg/inc/hdb.h
- lines changed 3, context: html, text, full: html, text
Two new tracks for Locus Reference Genomic (LRG) (#11863) with customhandlers: LRG Regions and LRG Transcripts.
LRGs are frozen reference sequences for a particular gene plus some
upstream and downstream sequence. They are intended to provide a
stable coordinate system for gene annotations that won't change
with every new genome assembly, but can be mapped to each genome
assembly. Since there is a lot of metadata associated with each
region, I made LRG Regions a bigBed 12 + with fields describing
mismatches and indels, so that PSL can be derived from the bigBed
and the original LRG sequence can be reconstructed using genome
assembly sequence and the mismatch/indel info. hgTracks shows
differences and LRG insertions into the reference assembly using
the cds.c baseColor code. (LRG deletions from the reference appear
as gaps, which we get for free with bed12 info).
For LRG Transcripts, I found the genePred codon-coloring code
inadequate for showing an insertion into hg19 (or even mismatches),
so instead of genePred I ended up using PSL + sequence, more like
the mRNA track representation and display.
- src/hg/inc/hui.h
- lines changed 7, context: html, text, full: html, text
Two new tracks for Locus Reference Genomic (LRG) (#11863) with customhandlers: LRG Regions and LRG Transcripts.
LRGs are frozen reference sequences for a particular gene plus some
upstream and downstream sequence. They are intended to provide a
stable coordinate system for gene annotations that won't change
with every new genome assembly, but can be mapped to each genome
assembly. Since there is a lot of metadata associated with each
region, I made LRG Regions a bigBed 12 + with fields describing
mismatches and indels, so that PSL can be derived from the bigBed
and the original LRG sequence can be reconstructed using genome
assembly sequence and the mismatch/indel info. hgTracks shows
differences and LRG insertions into the reference assembly using
the cds.c baseColor code. (LRG deletions from the reference appear
as gaps, which we get for free with bed12 info).
For LRG Transcripts, I found the genePred codon-coloring code
inadequate for showing an insertion into hg19 (or even mismatches),
so instead of genePred I ended up using PSL + sequence, more like
the mRNA track representation and display.
- src/hg/inc/lrg.h
- lines changed 109, context: html, text, full: html, text
Two new tracks for Locus Reference Genomic (LRG) (#11863) with customhandlers: LRG Regions and LRG Transcripts.
LRGs are frozen reference sequences for a particular gene plus some
upstream and downstream sequence. They are intended to provide a
stable coordinate system for gene annotations that won't change
with every new genome assembly, but can be mapped to each genome
assembly. Since there is a lot of metadata associated with each
region, I made LRG Regions a bigBed 12 + with fields describing
mismatches and indels, so that PSL can be derived from the bigBed
and the original LRG sequence can be reconstructed using genome
assembly sequence and the mismatch/indel info. hgTracks shows
differences and LRG insertions into the reference assembly using
the cds.c baseColor code. (LRG deletions from the reference appear
as gaps, which we get for free with bed12 info).
For LRG Transcripts, I found the genePred codon-coloring code
inadequate for showing an insertion into hg19 (or even mismatches),
so instead of genePred I ended up using PSL + sequence, more like
the mRNA track representation and display.
- src/hg/js/encodeProject.js
- lines changed 11, context: html, text, full: html, text
Switch to relative URL for Ajax call (fixes http vs https access problem. Also remove server config, which was used during testing but unused (and causes cross-site access issues)
- src/hg/js/hgVarAnnogrator.js
- lines changed 11, context: html, text, full: html, text
Work in progress for #11460 (paste/upload variant input options...):adding an option for user to paste/upload variant identifiers which
will be translated into a sorted list of vcfRecords.
Currently we recognize only rs# IDs. I was considering adding
dbVar IDs, but those could come from multiple sources (DGV, ClinVar,
ISCA) so I'm not sure.
Treating all symbolic/named alleles as deletions... non-ideal,
but fortunately those are a small minority in dbSNP.
Next: recognize HGVS IDs.
The grander vision of #11460 includes accepting VEP input format
and VCF, but I think those should be new SELECT options so we don't
get into quagmire of guessing format.
- src/hg/lib/annoFormatVep.c
- lines changed 13, context: html, text, full: html, text
Added comment method to annoFormatter.
- src/hg/lib/gpFx.c
- lines changed 9, context: html, text, full: html, text
Work in progress for #11460 (paste/upload variant input options...):adding an option for user to paste/upload variant identifiers which
will be translated into a sorted list of vcfRecords.
Currently we recognize only rs# IDs. I was considering adding
dbVar IDs, but those could come from multiple sources (DGV, ClinVar,
ISCA) so I'm not sure.
Treating all symbolic/named alleles as deletions... non-ideal,
but fortunately those are a small minority in dbSNP.
Next: recognize HGVS IDs.
The grander vision of #11460 includes accepting VEP input format
and VCF, but I think those should be new SELECT options so we don't
get into quagmire of guessing format.
- src/hg/lib/hdb.c
- lines changed 12, context: html, text, full: html, text
Two new tracks for Locus Reference Genomic (LRG) (#11863) with customhandlers: LRG Regions and LRG Transcripts.
LRGs are frozen reference sequences for a particular gene plus some
upstream and downstream sequence. They are intended to provide a
stable coordinate system for gene annotations that won't change
with every new genome assembly, but can be mapped to each genome
assembly. Since there is a lot of metadata associated with each
region, I made LRG Regions a bigBed 12 + with fields describing
mismatches and indels, so that PSL can be derived from the bigBed
and the original LRG sequence can be reconstructed using genome
assembly sequence and the mismatch/indel info. hgTracks shows
differences and LRG insertions into the reference assembly using
the cds.c baseColor code. (LRG deletions from the reference appear
as gaps, which we get for free with bed12 info).
For LRG Transcripts, I found the genePred codon-coloring code
inadequate for showing an insertion into hg19 (or even mismatches),
so instead of genePred I ended up using PSL + sequence, more like
the mRNA track representation and display.
- src/hg/lib/hui.c
- lines changed 49, context: html, text, full: html, text
Two new tracks for Locus Reference Genomic (LRG) (#11863) with customhandlers: LRG Regions and LRG Transcripts.
LRGs are frozen reference sequences for a particular gene plus some
upstream and downstream sequence. They are intended to provide a
stable coordinate system for gene annotations that won't change
with every new genome assembly, but can be mapped to each genome
assembly. Since there is a lot of metadata associated with each
region, I made LRG Regions a bigBed 12 + with fields describing
mismatches and indels, so that PSL can be derived from the bigBed
and the original LRG sequence can be reconstructed using genome
assembly sequence and the mismatch/indel info. hgTracks shows
differences and LRG insertions into the reference assembly using
the cds.c baseColor code. (LRG deletions from the reference appear
as gaps, which we get for free with bed12 info).
For LRG Transcripts, I found the genePred codon-coloring code
inadequate for showing an insertion into hg19 (or even mismatches),
so instead of genePred I ended up using PSL + sequence, more like
the mRNA track representation and display.
- src/hg/lib/lrg.as
- lines changed 25, context: html, text, full: html, text
Two new tracks for Locus Reference Genomic (LRG) (#11863) with customhandlers: LRG Regions and LRG Transcripts.
LRGs are frozen reference sequences for a particular gene plus some
upstream and downstream sequence. They are intended to provide a
stable coordinate system for gene annotations that won't change
with every new genome assembly, but can be mapped to each genome
assembly. Since there is a lot of metadata associated with each
region, I made LRG Regions a bigBed 12 + with fields describing
mismatches and indels, so that PSL can be derived from the bigBed
and the original LRG sequence can be reconstructed using genome
assembly sequence and the mismatch/indel info. hgTracks shows
differences and LRG insertions into the reference assembly using
the cds.c baseColor code. (LRG deletions from the reference appear
as gaps, which we get for free with bed12 info).
For LRG Transcripts, I found the genePred codon-coloring code
inadequate for showing an insertion into hg19 (or even mismatches),
so instead of genePred I ended up using PSL + sequence, more like
the mRNA track representation and display.
- src/hg/lib/lrg.c
- lines changed 480, context: html, text, full: html, text
Two new tracks for Locus Reference Genomic (LRG) (#11863) with customhandlers: LRG Regions and LRG Transcripts.
LRGs are frozen reference sequences for a particular gene plus some
upstream and downstream sequence. They are intended to provide a
stable coordinate system for gene annotations that won't change
with every new genome assembly, but can be mapped to each genome
assembly. Since there is a lot of metadata associated with each
region, I made LRG Regions a bigBed 12 + with fields describing
mismatches and indels, so that PSL can be derived from the bigBed
and the original LRG sequence can be reconstructed using genome
assembly sequence and the mismatch/indel info. hgTracks shows
differences and LRG insertions into the reference assembly using
the cds.c baseColor code. (LRG deletions from the reference appear
as gaps, which we get for free with bed12 info).
For LRG Transcripts, I found the genePred codon-coloring code
inadequate for showing an insertion into hg19 (or even mismatches),
so instead of genePred I ended up using PSL + sequence, more like
the mRNA track representation and display.
- src/hg/lib/makefile
- lines changed 1, context: html, text, full: html, text
Two new tracks for Locus Reference Genomic (LRG) (#11863) with customhandlers: LRG Regions and LRG Transcripts.
LRGs are frozen reference sequences for a particular gene plus some
upstream and downstream sequence. They are intended to provide a
stable coordinate system for gene annotations that won't change
with every new genome assembly, but can be mapped to each genome
assembly. Since there is a lot of metadata associated with each
region, I made LRG Regions a bigBed 12 + with fields describing
mismatches and indels, so that PSL can be derived from the bigBed
and the original LRG sequence can be reconstructed using genome
assembly sequence and the mismatch/indel info. hgTracks shows
differences and LRG insertions into the reference assembly using
the cds.c baseColor code. (LRG deletions from the reference appear
as gaps, which we get for free with bed12 info).
For LRG Transcripts, I found the genePred codon-coloring code
inadequate for showing an insertion into hg19 (or even mismatches),
so instead of genePred I ended up using PSL + sequence, more like
the mRNA track representation and display.
- src/hg/liftOver/tests/makefile
- lines changed 14, context: html, text, full: html, text
silent test output unless errors refs #12090
- src/hg/makeDb/doc/hg19.txt
- lines changed 70, context: html, text, full: html, text
Two new tracks for Locus Reference Genomic (LRG) (#11863) with customhandlers: LRG Regions and LRG Transcripts.
LRGs are frozen reference sequences for a particular gene plus some
upstream and downstream sequence. They are intended to provide a
stable coordinate system for gene annotations that won't change
with every new genome assembly, but can be mapped to each genome
assembly. Since there is a lot of metadata associated with each
region, I made LRG Regions a bigBed 12 + with fields describing
mismatches and indels, so that PSL can be derived from the bigBed
and the original LRG sequence can be reconstructed using genome
assembly sequence and the mismatch/indel info. hgTracks shows
differences and LRG insertions into the reference assembly using
the cds.c baseColor code. (LRG deletions from the reference appear
as gaps, which we get for free with bed12 info).
For LRG Transcripts, I found the genePred codon-coloring code
inadequate for showing an insertion into hg19 (or even mismatches),
so instead of genePred I ended up using PSL + sequence, more like
the mRNA track representation and display.
- src/hg/makeDb/doc/macEug2.txt
- lines changed 12, context: html, text, full: html, text
document finish of genscan2 refs #7272
- src/hg/makeDb/schema/all.joiner
- lines changed 1, context: html, text, full: html, text
Two new tracks for Locus Reference Genomic (LRG) (#11863) with customhandlers: LRG Regions and LRG Transcripts.
LRGs are frozen reference sequences for a particular gene plus some
upstream and downstream sequence. They are intended to provide a
stable coordinate system for gene annotations that won't change
with every new genome assembly, but can be mapped to each genome
assembly. Since there is a lot of metadata associated with each
region, I made LRG Regions a bigBed 12 + with fields describing
mismatches and indels, so that PSL can be derived from the bigBed
and the original LRG sequence can be reconstructed using genome
assembly sequence and the mismatch/indel info. hgTracks shows
differences and LRG insertions into the reference assembly using
the cds.c baseColor code. (LRG deletions from the reference appear
as gaps, which we get for free with bed12 info).
For LRG Transcripts, I found the genePred codon-coloring code
inadequate for showing an insertion into hg19 (or even mismatches),
so instead of genePred I ended up using PSL + sequence, more like
the mRNA track representation and display.
- src/hg/makeDb/trackDb/human/lrg.html
- lines changed 50, context: html, text, full: html, text
Two new tracks for Locus Reference Genomic (LRG) (#11863) with customhandlers: LRG Regions and LRG Transcripts.
LRGs are frozen reference sequences for a particular gene plus some
upstream and downstream sequence. They are intended to provide a
stable coordinate system for gene annotations that won't change
with every new genome assembly, but can be mapped to each genome
assembly. Since there is a lot of metadata associated with each
region, I made LRG Regions a bigBed 12 + with fields describing
mismatches and indels, so that PSL can be derived from the bigBed
and the original LRG sequence can be reconstructed using genome
assembly sequence and the mismatch/indel info. hgTracks shows
differences and LRG insertions into the reference assembly using
the cds.c baseColor code. (LRG deletions from the reference appear
as gaps, which we get for free with bed12 info).
For LRG Transcripts, I found the genePred codon-coloring code
inadequate for showing an insertion into hg19 (or even mismatches),
so instead of genePred I ended up using PSL + sequence, more like
the mRNA track representation and display.
- lines changed 11, context: html, text, full: html, text
Updated descriptions of LRG tracks with info from Fiona Cunningham at EBI.refs #11863
- src/hg/makeDb/trackDb/human/lrgTranscriptAli.html
- lines changed 54, context: html, text, full: html, text
Two new tracks for Locus Reference Genomic (LRG) (#11863) with customhandlers: LRG Regions and LRG Transcripts.
LRGs are frozen reference sequences for a particular gene plus some
upstream and downstream sequence. They are intended to provide a
stable coordinate system for gene annotations that won't change
with every new genome assembly, but can be mapped to each genome
assembly. Since there is a lot of metadata associated with each
region, I made LRG Regions a bigBed 12 + with fields describing
mismatches and indels, so that PSL can be derived from the bigBed
and the original LRG sequence can be reconstructed using genome
assembly sequence and the mismatch/indel info. hgTracks shows
differences and LRG insertions into the reference assembly using
the cds.c baseColor code. (LRG deletions from the reference appear
as gaps, which we get for free with bed12 info).
For LRG Transcripts, I found the genePred codon-coloring code
inadequate for showing an insertion into hg19 (or even mismatches),
so instead of genePred I ended up using PSL + sequence, more like
the mRNA track representation and display.
- lines changed 9, context: html, text, full: html, text
Updated descriptions of LRG tracks with info from Fiona Cunningham at EBI.refs #11863
- src/hg/makeDb/trackDb/human/phastBias.html
- lines changed 1, context: html, text, full: html, text
Changing reference link to point to the free abstract per Code Review, refs #12135
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 46, context: html, text, full: html, text
Two new tracks for Locus Reference Genomic (LRG) (#11863) with customhandlers: LRG Regions and LRG Transcripts.
LRGs are frozen reference sequences for a particular gene plus some
upstream and downstream sequence. They are intended to provide a
stable coordinate system for gene annotations that won't change
with every new genome assembly, but can be mapped to each genome
assembly. Since there is a lot of metadata associated with each
region, I made LRG Regions a bigBed 12 + with fields describing
mismatches and indels, so that PSL can be derived from the bigBed
and the original LRG sequence can be reconstructed using genome
assembly sequence and the mismatch/indel info. hgTracks shows
differences and LRG insertions into the reference assembly using
the cds.c baseColor code. (LRG deletions from the reference appear
as gaps, which we get for free with bed12 info).
For LRG Transcripts, I found the genePred codon-coloring code
inadequate for showing an insertion into hg19 (or even mismatches),
so instead of genePred I ended up using PSL + sequence, more like
the mRNA track representation and display.
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
- lines changed 13, context: html, text, full: html, text
Added entry for lifted jaxQtl track. refs #7040
- src/hg/makeDb/trackDb/tagTypes.tab
- lines changed 5, context: html, text, full: html, text
Two new tracks for Locus Reference Genomic (LRG) (#11863) with customhandlers: LRG Regions and LRG Transcripts.
LRGs are frozen reference sequences for a particular gene plus some
upstream and downstream sequence. They are intended to provide a
stable coordinate system for gene annotations that won't change
with every new genome assembly, but can be mapped to each genome
assembly. Since there is a lot of metadata associated with each
region, I made LRG Regions a bigBed 12 + with fields describing
mismatches and indels, so that PSL can be derived from the bigBed
and the original LRG sequence can be reconstructed using genome
assembly sequence and the mismatch/indel info. hgTracks shows
differences and LRG insertions into the reference assembly using
the cds.c baseColor code. (LRG deletions from the reference appear
as gaps, which we get for free with bed12 info).
For LRG Transcripts, I found the genePred codon-coloring code
inadequate for showing an insertion into hg19 (or even mismatches),
so instead of genePred I ended up using PSL + sequence, more like
the mRNA track representation and display.
- src/hg/makefile
- lines changed 6, context: html, text, full: html, text
adding more tests when they can be found refs #9149
- src/hg/utils/automation/parseLrgXml.pl
- lines changed 221, context: html, text, full: html, text
Two new tracks for Locus Reference Genomic (LRG) (#11863) with customhandlers: LRG Regions and LRG Transcripts.
LRGs are frozen reference sequences for a particular gene plus some
upstream and downstream sequence. They are intended to provide a
stable coordinate system for gene annotations that won't change
with every new genome assembly, but can be mapped to each genome
assembly. Since there is a lot of metadata associated with each
region, I made LRG Regions a bigBed 12 + with fields describing
mismatches and indels, so that PSL can be derived from the bigBed
and the original LRG sequence can be reconstructed using genome
assembly sequence and the mismatch/indel info. hgTracks shows
differences and LRG insertions into the reference assembly using
the cds.c baseColor code. (LRG deletions from the reference appear
as gaps, which we get for free with bed12 info).
For LRG Transcripts, I found the genePred codon-coloring code
inadequate for showing an insertion into hg19 (or even mismatches),
so instead of genePred I ended up using PSL + sequence, more like
the mRNA track representation and display.
- src/hg/utils/lrgToPsl/lrgToPsl.c
- lines changed 51, context: html, text, full: html, text
Two new tracks for Locus Reference Genomic (LRG) (#11863) with customhandlers: LRG Regions and LRG Transcripts.
LRGs are frozen reference sequences for a particular gene plus some
upstream and downstream sequence. They are intended to provide a
stable coordinate system for gene annotations that won't change
with every new genome assembly, but can be mapped to each genome
assembly. Since there is a lot of metadata associated with each
region, I made LRG Regions a bigBed 12 + with fields describing
mismatches and indels, so that PSL can be derived from the bigBed
and the original LRG sequence can be reconstructed using genome
assembly sequence and the mismatch/indel info. hgTracks shows
differences and LRG insertions into the reference assembly using
the cds.c baseColor code. (LRG deletions from the reference appear
as gaps, which we get for free with bed12 info).
For LRG Transcripts, I found the genePred codon-coloring code
inadequate for showing an insertion into hg19 (or even mismatches),
so instead of genePred I ended up using PSL + sequence, more like
the mRNA track representation and display.
- src/hg/utils/lrgToPsl/makefile
- lines changed 3, context: html, text, full: html, text
Two new tracks for Locus Reference Genomic (LRG) (#11863) with customhandlers: LRG Regions and LRG Transcripts.
LRGs are frozen reference sequences for a particular gene plus some
upstream and downstream sequence. They are intended to provide a
stable coordinate system for gene annotations that won't change
with every new genome assembly, but can be mapped to each genome
assembly. Since there is a lot of metadata associated with each
region, I made LRG Regions a bigBed 12 + with fields describing
mismatches and indels, so that PSL can be derived from the bigBed
and the original LRG sequence can be reconstructed using genome
assembly sequence and the mismatch/indel info. hgTracks shows
differences and LRG insertions into the reference assembly using
the cds.c baseColor code. (LRG deletions from the reference appear
as gaps, which we get for free with bed12 info).
For LRG Transcripts, I found the genePred codon-coloring code
inadequate for showing an insertion into hg19 (or even mismatches),
so instead of genePred I ended up using PSL + sequence, more like
the mRNA track representation and display.
- src/hg/utils/tdbQuery/tdbQuery.c
- lines changed 5, context: html, text, full: html, text
Fixed output of extraneous blank lines refs #12159
- src/inc/annoFormatter.h
- lines changed 3, context: html, text, full: html, text
Added comment method to annoFormatter.
- src/inc/dnautil.h
- lines changed 5, context: html, text, full: html, text
isAllDna has a condition that surprised me (returns FALSE if size is 1),so I added isAllNt which has the behavior I expected.
- src/inc/hash.h
- lines changed 4, context: html, text, full: html, text
Two new tracks for Locus Reference Genomic (LRG) (#11863) with customhandlers: LRG Regions and LRG Transcripts.
LRGs are frozen reference sequences for a particular gene plus some
upstream and downstream sequence. They are intended to provide a
stable coordinate system for gene annotations that won't change
with every new genome assembly, but can be mapped to each genome
assembly. Since there is a lot of metadata associated with each
region, I made LRG Regions a bigBed 12 + with fields describing
mismatches and indels, so that PSL can be derived from the bigBed
and the original LRG sequence can be reconstructed using genome
assembly sequence and the mismatch/indel info. hgTracks shows
differences and LRG insertions into the reference assembly using
the cds.c baseColor code. (LRG deletions from the reference appear
as gaps, which we get for free with bed12 info).
For LRG Transcripts, I found the genePred codon-coloring code
inadequate for showing an insertion into hg19 (or even mismatches),
so instead of genePred I ended up using PSL + sequence, more like
the mRNA track representation and display.
- src/inc/htmlPage.h
- lines changed 4, context: html, text, full: html, text
Added new function findNextMatchingTag() to htmlPage.c
struct htmlTag *findNextMatchingTag(struct htmlTag *list, char *name);
/* Return first tag in list that is of type name or NULL if not found.
* */
- src/inc/md5.h
- src/inc/vcf.h
- lines changed 6, context: html, text, full: html, text
Work in progress for #11460 (paste/upload variant input options...):adding an option for user to paste/upload variant identifiers which
will be translated into a sorted list of vcfRecords.
Currently we recognize only rs# IDs. I was considering adding
dbVar IDs, but those could come from multiple sources (DGV, ClinVar,
ISCA) so I'm not sure.
Treating all symbolic/named alleles as deletions... non-ideal,
but fortunately those are a small minority in dbSNP.
Next: recognize HGVS IDs.
The grander vision of #11460 includes accepting VEP input format
and VCF, but I think those should be new SELECT options so we don't
get into quagmire of guessing format.
- src/lib/annoFormatTab.c
- lines changed 10, context: html, text, full: html, text
Added comment method to annoFormatter.
- src/lib/dnautil.c
- lines changed 15, context: html, text, full: html, text
isAllDna has a condition that surprised me (returns FALSE if size is 1),so I added isAllNt which has the behavior I expected.
- src/lib/hash.c
- lines changed 19, context: html, text, full: html, text
Two new tracks for Locus Reference Genomic (LRG) (#11863) with customhandlers: LRG Regions and LRG Transcripts.
LRGs are frozen reference sequences for a particular gene plus some
upstream and downstream sequence. They are intended to provide a
stable coordinate system for gene annotations that won't change
with every new genome assembly, but can be mapped to each genome
assembly. Since there is a lot of metadata associated with each
region, I made LRG Regions a bigBed 12 + with fields describing
mismatches and indels, so that PSL can be derived from the bigBed
and the original LRG sequence can be reconstructed using genome
assembly sequence and the mismatch/indel info. hgTracks shows
differences and LRG insertions into the reference assembly using
the cds.c baseColor code. (LRG deletions from the reference appear
as gaps, which we get for free with bed12 info).
For LRG Transcripts, I found the genePred codon-coloring code
inadequate for showing an insertion into hg19 (or even mismatches),
so instead of genePred I ended up using PSL + sequence, more like
the mRNA track representation and display.
- src/lib/htmlPage.c
- lines changed 12, context: html, text, full: html, text
Added new function findNextMatchingTag() to htmlPage.c
struct htmlTag *findNextMatchingTag(struct htmlTag *list, char *name);
/* Return first tag in list that is of type name or NULL if not found.
* */
- src/lib/md5.c
- src/lib/twoBit.c
- lines changed 5, context: html, text, full: html, text
new 5.0 gcc compiler on mac OSX will not accept bare inline functions must be static inline instead refs #12106
- src/lib/vcf.c
- lines changed 24, context: html, text, full: html, text
Work in progress for #11460 (paste/upload variant input options...):adding an option for user to paste/upload variant identifiers which
will be translated into a sorted list of vcfRecords.
Currently we recognize only rs# IDs. I was considering adding
dbVar IDs, but those could come from multiple sources (DGV, ClinVar,
ISCA) so I'm not sure.
Treating all symbolic/named alleles as deletions... non-ideal,
but fortunately those are a small minority in dbSNP.
Next: recognize HGVS IDs.
The grander vision of #11460 includes accepting VEP input format
and VCF, but I think those should be new SELECT options so we don't
get into quagmire of guessing format.
- src/makefile
- lines changed 1, context: html, text, full: html, text
adding utils directory to the test targets refs #9149
- src/parasol/makefile
- lines changed 1, context: html, text, full: html, text
include localEnvironment.mk so that a local make will work in userApps build refs #9149
- src/product/README.customTracks.dataBase
- lines changed 1, context: html, text, full: html, text
Adding central.db=hgcentral line to places where we explain needed .hg.conf refs #12170
- src/product/README.mysql.setup
- lines changed 1, context: html, text, full: html, text
Adding central.db=hgcentral line to places where we explain needed .hg.conf refs #12170
- src/userApps/README
- lines changed 1, context: html, text, full: html, text
Adding central.db=hgcentral line to places where we explain needed .hg.conf refs #12170
- src/utils/faRandomize/tests/makefile
- lines changed 5, context: html, text, full: html, text
silent test output unless errors refs #12090
- src/utils/makefile
- lines changed 7, context: html, text, full: html, text
running any test that can be found refs #9149
- lines changed 1, context: html, text, full: html, text
do not need the OK message on the testAll procedure refs #9149
- src/utils/qa/findLevel
- lines changed 107, context: html, text, full: html, text
findLevel now handles alternate html files, plus has a hopefully more extensible design
- src/utils/qa/weeklybld/buildEnv.csh
- src/utils/twoBitToFa/tests/expected/bed_ml_partial_list.fa
- lines changed 2, context: html, text, full: html, text
fixup correct expected test result refs #9149
- src/utils/userApps/mkREADME.sh
- lines changed 8, context: html, text, full: html, text
add note about rsync the entire directory to download binaries refs #12165
- lines changed: 2660
- files changed: 77