File Changes for angie
switch to commits view, user indexv306_preview to v306_preview2 (2014-09-08 to 2014-09-15) v306
- src/hg/hgTracks/variation.c
- lines changed 20, context: html, text, full: html, text
Changes to snpNcbiToUcsc to handle b141 on hg19 and hg38:- When checking range{I,D,S}* locTypes, use strlen(refNCBI) as length only if
refNCBI contains only nucleotides.
- Checking for overlapping variants at the same location (checkCluster ->
DuplicateObserved, MixedObserved) used to be limited to insertions because
those are easier to check. Now we check all variants that have
all-nucleotide observed. Libified some code from hgTracks that can
reverse-complement a slash-separated string of alleles, e.g. G/T -> A/C,
-/AG -> -/CT.
- SNP IDs are getting too huge (and sparse) to use as indexes into a
statically allocated array; use a hash.
- Erroneous NULL frequencies in dbSNP's SNPAlleleFreq need to be detected
and ignored.
refs #13309
- src/hg/hgTracks/wigMafTrack.c
- lines changed 64, context: html, text, full: html, text
Removing dead code for "useTarg" (#ifndef'd out with BRANEY_SAYS_USETARG_IS_OBSOLETE).
- src/hg/lib/hui.c
- lines changed 36, context: html, text, full: html, text
Removing dead code for "useTarg" (#ifndef'd out with BRANEY_SAYS_USETARG_IS_OBSOLETE).
- src/hg/makeDb/doc/eboVir2/gire.txt
- lines changed 109, context: html, text, full: html, text
Added a couple VCF tracks from Gire et al (99 samples from 78 patients,variants called with other Zaire-clade ebola viruses).
- src/hg/makeDb/doc/eboVir2/multizLabels.txt
- lines changed 84, context: html, text, full: html, text
Added eboVir2.multiz49wayStrainNames, which is multiz49way.maf with strain names from http://epidemic.bio.ed.ac.uk/ebolavirus_sequences
- src/hg/makeDb/doc/hg19.txt
- lines changed 531, context: html, text, full: html, text
SNPs(141) tracks (dbSNP b141, released for both hg19 and hg38).refs #13309
- src/hg/makeDb/doc/hg38.txt
- lines changed 542, context: html, text, full: html, text
SNPs(141) tracks (dbSNP b141, released for both hg19 and hg38).refs #13309
- src/hg/makeDb/schema/all.joiner
- lines changed 12, context: html, text, full: html, text
SNPs(141) tracks (dbSNP b141, released for both hg19 and hg38).refs #13309
- src/hg/makeDb/trackDb/ebola/eboVir2/gireZebov.html
- lines changed 12, context: html, text, full: html, text
Added a couple VCF tracks from Gire et al (99 samples from 78 patients,variants called with other Zaire-clade ebola viruses).
- src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.49way.ra
- lines changed 1, context: html, text, full: html, text
Added eboVir2.multiz49wayStrainNames, which is multiz49way.maf with strain names from http://epidemic.bio.ed.ac.uk/ebolavirus_sequences
- src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.49wayStrainNames.ra
- lines changed 37, context: html, text, full: html, text
Added eboVir2.multiz49wayStrainNames, which is multiz49way.maf with strain names from http://epidemic.bio.ed.ac.uk/ebolavirus_sequences
- src/hg/makeDb/trackDb/ebola/eboVir2/trackDb.ra
- lines changed 1, context: html, text, full: html, text
Added eboVir2.multiz49wayStrainNames, which is multiz49way.maf with strain names from http://epidemic.bio.ed.ac.uk/ebolavirus_sequences
- lines changed 14, context: html, text, full: html, text
Added a couple VCF tracks from Gire et al (99 samples from 78 patients,variants called with other Zaire-clade ebola viruses).
- lines changed 1, context: html, text, full: html, text
Making gireZebov visible by default.
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 3, context: html, text, full: html, text
Removing snp141Mult track from hg19/trackDb.ra... there are no Mults in hg19 snp141!refs #13309
- src/hg/makeDb/trackDb/human/hg38/trackDb.ra
- src/hg/snp/snpLoad/snpNcbiToUcsc.c
- lines changed 123, context: html, text, full: html, text
Changes to snpNcbiToUcsc to handle b141 on hg19 and hg38:- When checking range{I,D,S}* locTypes, use strlen(refNCBI) as length only if
refNCBI contains only nucleotides.
- Checking for overlapping variants at the same location (checkCluster ->
DuplicateObserved, MixedObserved) used to be limited to insertions because
those are easier to check. Now we check all variants that have
all-nucleotide observed. Libified some code from hgTracks that can
reverse-complement a slash-separated string of alleles, e.g. G/T -> A/C,
-/AG -> -/CT.
- SNP IDs are getting too huge (and sparse) to use as indexes into a
statically allocated array; use a hash.
- Erroneous NULL frequencies in dbSNP's SNPAlleleFreq need to be detected
and ignored.
refs #13309
- src/hg/utils/automation/doDbSnp.pl
- lines changed 101, context: html, text, full: html, text
Changes to support dbSNP b141, released on both hg19 and hg38:- Support multiple assemblies of the same organism in a single build.
- Support strange one-off orgDir like human_9606_b141_GRCh37p13.
- Added 'filter' step to extract snpNNN{Common,Mult,Flagged} sets and load tables.
- Added coding step to make snpNNNCodingDbSnp table.
refs #13309
- src/inc/dnautil.h
- lines changed 5, context: html, text, full: html, text
Changes to snpNcbiToUcsc to handle b141 on hg19 and hg38:- When checking range{I,D,S}* locTypes, use strlen(refNCBI) as length only if
refNCBI contains only nucleotides.
- Checking for overlapping variants at the same location (checkCluster ->
DuplicateObserved, MixedObserved) used to be limited to insertions because
those are easier to check. Now we check all variants that have
all-nucleotide observed. Libified some code from hgTracks that can
reverse-complement a slash-separated string of alleles, e.g. G/T -> A/C,
-/AG -> -/CT.
- SNP IDs are getting too huge (and sparse) to use as indexes into a
statically allocated array; use a hash.
- Erroneous NULL frequencies in dbSNP's SNPAlleleFreq need to be detected
and ignored.
refs #13309
- src/lib/dnautil.c
- lines changed 35, context: html, text, full: html, text
Changes to snpNcbiToUcsc to handle b141 on hg19 and hg38:- When checking range{I,D,S}* locTypes, use strlen(refNCBI) as length only if
refNCBI contains only nucleotides.
- Checking for overlapping variants at the same location (checkCluster ->
DuplicateObserved, MixedObserved) used to be limited to insertions because
those are easier to check. Now we check all variants that have
all-nucleotide observed. Libified some code from hgTracks that can
reverse-complement a slash-separated string of alleles, e.g. G/T -> A/C,
-/AG -> -/CT.
- SNP IDs are getting too huge (and sparse) to use as indexes into a
statically allocated array; use a hash.
- Erroneous NULL frequencies in dbSNP's SNPAlleleFreq need to be detected
and ignored.
refs #13309
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