File Changes for angie
switch to commits view, user indexv292_base to v293_preview (2013-11-11 to 2013-11-18) v293
- 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/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/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/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/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/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/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/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/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/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/md5.c
- 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.
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