All File Changes
v323_preview2 to v323_base (2015-09-28 to 2015-10-05) v323
- src/ameme/ameme.c
- lines changed 6, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/ameme/fragFind.c
- lines changed 4, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/hg/cartReset/cartReset.c
- lines changed 8, context: html, text, full: html, text
Removing message and redirect link from cartReset as requested. Fixes #8949.
- src/hg/encode3/validateFiles/validateFiles.c
- lines changed 6, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/hg/encode3/validateManifest/validateManifest.c
- lines changed 2, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/hg/featureBits/featureBits.c
- lines changed 3, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/hg/getRnaPred/getRnaPred.c
- lines changed 2, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/hg/hgGene/hgGeneData/Human/hg19/links.ra
- lines changed 6, context: html, text, full: html, text
Removing assembly level links for GTEx (handled at Human level). refs #15649
- src/hg/hgGene/hgGeneData/Human/hg38/links.ra
- lines changed 8, context: html, text, full: html, text
Removing assembly level links for GTEx (handled at Human level). refs #15649
- src/hg/htdocs/goldenPath/help/customTrackText.html
- lines changed 14, context: html, text, full: html, text
adding docs for URL parameters
- lines changed 1, context: html, text, full: html, text
adding highlight suggested by BrianR
- lines changed 3, context: html, text, full: html, text
adding hgRenderTracks note to URL documentation, may be useful in this
context, refs #16106
- src/hg/inc/versionInfo.h
- src/hg/lib/agp.c
- lines changed 34, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/hg/lib/altGraphX.c
- lines changed 8, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/hg/lib/annoStreamDb.c
- lines changed 164, context: html, text, full: html, text
Add test cases (and bug fixes!) to make sure that we get the desired
behavior when an insertion is adjacent to a non-insertion, and when
an insertion falls at the start or end of the search region (if applicable):
- Include insertions that fall at the start or end of the search region
- If the primary row is an insertion, keep secondary non-insertion rows
to the left and right.
- If the primary row is a non-insertion, keep secondary insertion rows
at its start and end.
(i.e. keep insertions at boundaries -- but don't let any non-insertions
slip through)
The VCF logic is more complicated because VCF indels always include an
extra base to the left, so they appear to start before they actually do,
and can be interspersed with non-indels that start there.
- src/hg/lib/bed.sql
- lines changed 1, context: html, text, full: html, text
Add test cases (and bug fixes!) to make sure that we get the desired
behavior when an insertion is adjacent to a non-insertion, and when
an insertion falls at the start or end of the search region (if applicable):
- Include insertions that fall at the start or end of the search region
- If the primary row is an insertion, keep secondary non-insertion rows
to the left and right.
- If the primary row is a non-insertion, keep secondary insertion rows
at its start and end.
(i.e. keep insertions at boundaries -- but don't let any non-insertions
slip through)
The VCF logic is more complicated because VCF indels always include an
extra base to the left, so they appear to start before they actually do,
and can be interspersed with non-indels that start there.
- src/hg/lib/bedDetail.c
- lines changed 5, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/hg/lib/borf.c
- lines changed 2, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/hg/lib/cart.c
- lines changed 2, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/hg/lib/customFactory.c
- lines changed 8, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/hg/lib/decipherRaw.sql
- lines changed 1, context: html, text, full: html, text
add an index to the decipherRaw file #16107
- src/hg/lib/genoLay.c
- lines changed 4, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/hg/lib/ggCluster.c
- lines changed 1, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/hg/lib/hdb.c
- lines changed 6, context: html, text, full: html, text
hFindTableInfoWithConn was checking table existence when chrom was given,
but not when chrom was NULL, and so it failed to check existence for a
table when looking in hgFixed. Now it always checks existence.
Also, it uses hTableExists (cached) instead of sqlTableExists.
refs #16112
- src/hg/lib/hgFind.c
- lines changed 12, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/hg/lib/hgFindSpecCustom.c
- lines changed 3, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/hg/lib/hui.c
- lines changed 14, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/hg/lib/rmskOut.c
- lines changed 5, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/hg/lib/rmskOut2.c
- lines changed 2, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/hg/lib/sqlProg.c
- lines changed 3, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/hg/lib/tests/annoGratorTester.c
- lines changed 64, context: html, text, full: html, text
Add test cases (and bug fixes!) to make sure that we get the desired
behavior when an insertion is adjacent to a non-insertion, and when
an insertion falls at the start or end of the search region (if applicable):
- Include insertions that fall at the start or end of the search region
- If the primary row is an insertion, keep secondary non-insertion rows
to the left and right.
- If the primary row is a non-insertion, keep secondary insertion rows
at its start and end.
(i.e. keep insertions at boundaries -- but don't let any non-insertions
slip through)
The VCF logic is more complicated because VCF indels always include an
extra base to the left, so they appear to start before they actually do,
and can be interspersed with non-indels that start there.
- lines changed 10, context: html, text, full: html, text
Test & fix VCF+tabix querying of insertion items.
- src/hg/lib/tests/annoGratorTests.mk
- lines changed 15, context: html, text, full: html, text
Add test cases (and bug fixes!) to make sure that we get the desired
behavior when an insertion is adjacent to a non-insertion, and when
an insertion falls at the start or end of the search region (if applicable):
- Include insertions that fall at the start or end of the search region
- If the primary row is an insertion, keep secondary non-insertion rows
to the left and right.
- If the primary row is a non-insertion, keep secondary insertion rows
at its start and end.
(i.e. keep insertions at boundaries -- but don't let any non-insertions
slip through)
The VCF logic is more complicated because VCF indels always include an
extra base to the left, so they appear to start before they actually do,
and can be interspersed with non-indels that start there.
- src/hg/lib/tests/expected/annoGrator/insertions.txt
- lines changed 212, context: html, text, full: html, text
Add test cases (and bug fixes!) to make sure that we get the desired
behavior when an insertion is adjacent to a non-insertion, and when
an insertion falls at the start or end of the search region (if applicable):
- Include insertions that fall at the start or end of the search region
- If the primary row is an insertion, keep secondary non-insertion rows
to the left and right.
- If the primary row is a non-insertion, keep secondary insertion rows
at its start and end.
(i.e. keep insertions at boundaries -- but don't let any non-insertions
slip through)
The VCF logic is more complicated because VCF indels always include an
extra base to the left, so they appear to start before they actually do,
and can be interspersed with non-indels that start there.
- lines changed 4, context: html, text, full: html, text
Added another test case: first item in primary is an insertion and first item
in secondary is adjacent on the left.
- lines changed 96, context: html, text, full: html, text
Test & fix VCF+tabix querying of insertion items.
- src/hg/lib/tests/input/annoGrator/insertionsPrimary.bb
- lines changed 0, context: html, text, full: html, text
Add test cases (and bug fixes!) to make sure that we get the desired
behavior when an insertion is adjacent to a non-insertion, and when
an insertion falls at the start or end of the search region (if applicable):
- Include insertions that fall at the start or end of the search region
- If the primary row is an insertion, keep secondary non-insertion rows
to the left and right.
- If the primary row is a non-insertion, keep secondary insertion rows
at its start and end.
(i.e. keep insertions at boundaries -- but don't let any non-insertions
slip through)
The VCF logic is more complicated because VCF indels always include an
extra base to the left, so they appear to start before they actually do,
and can be interspersed with non-indels that start there.
- lines changed 0, context: html, text, full: html, text
Added another test case: first item in primary is an insertion and first item
in secondary is adjacent on the left.
- src/hg/lib/tests/input/annoGrator/insertionsPrimary.bed
- lines changed 16, context: html, text, full: html, text
Add test cases (and bug fixes!) to make sure that we get the desired
behavior when an insertion is adjacent to a non-insertion, and when
an insertion falls at the start or end of the search region (if applicable):
- Include insertions that fall at the start or end of the search region
- If the primary row is an insertion, keep secondary non-insertion rows
to the left and right.
- If the primary row is a non-insertion, keep secondary insertion rows
at its start and end.
(i.e. keep insertions at boundaries -- but don't let any non-insertions
slip through)
The VCF logic is more complicated because VCF indels always include an
extra base to the left, so they appear to start before they actually do,
and can be interspersed with non-indels that start there.
- lines changed 2, context: html, text, full: html, text
Added another test case: first item in primary is an insertion and first item
in secondary is adjacent on the left.
- src/hg/lib/tests/input/annoGrator/insertionsPrimary.vcf
- lines changed 18, context: html, text, full: html, text
Add test cases (and bug fixes!) to make sure that we get the desired
behavior when an insertion is adjacent to a non-insertion, and when
an insertion falls at the start or end of the search region (if applicable):
- Include insertions that fall at the start or end of the search region
- If the primary row is an insertion, keep secondary non-insertion rows
to the left and right.
- If the primary row is a non-insertion, keep secondary insertion rows
at its start and end.
(i.e. keep insertions at boundaries -- but don't let any non-insertions
slip through)
The VCF logic is more complicated because VCF indels always include an
extra base to the left, so they appear to start before they actually do,
and can be interspersed with non-indels that start there.
- lines changed 9, context: html, text, full: html, text
Added another test case: first item in primary is an insertion and first item
in secondary is adjacent on the left.
- src/hg/lib/tests/input/annoGrator/insertionsPrimary.vcf.gz
- lines changed 0, context: html, text, full: html, text
Test & fix VCF+tabix querying of insertion items.
- src/hg/lib/tests/input/annoGrator/insertionsPrimary.vcf.gz.tbi
- lines changed 0, context: html, text, full: html, text
Test & fix VCF+tabix querying of insertion items.
- src/hg/lib/tests/input/annoGrator/insertionsSecondary.bb
- lines changed 0, context: html, text, full: html, text
Add test cases (and bug fixes!) to make sure that we get the desired
behavior when an insertion is adjacent to a non-insertion, and when
an insertion falls at the start or end of the search region (if applicable):
- Include insertions that fall at the start or end of the search region
- If the primary row is an insertion, keep secondary non-insertion rows
to the left and right.
- If the primary row is a non-insertion, keep secondary insertion rows
at its start and end.
(i.e. keep insertions at boundaries -- but don't let any non-insertions
slip through)
The VCF logic is more complicated because VCF indels always include an
extra base to the left, so they appear to start before they actually do,
and can be interspersed with non-indels that start there.
- lines changed 0, context: html, text, full: html, text
Added another test case: first item in primary is an insertion and first item
in secondary is adjacent on the left.
- src/hg/lib/tests/input/annoGrator/insertionsSecondary.bed
- lines changed 25, context: html, text, full: html, text
Add test cases (and bug fixes!) to make sure that we get the desired
behavior when an insertion is adjacent to a non-insertion, and when
an insertion falls at the start or end of the search region (if applicable):
- Include insertions that fall at the start or end of the search region
- If the primary row is an insertion, keep secondary non-insertion rows
to the left and right.
- If the primary row is a non-insertion, keep secondary insertion rows
at its start and end.
(i.e. keep insertions at boundaries -- but don't let any non-insertions
slip through)
The VCF logic is more complicated because VCF indels always include an
extra base to the left, so they appear to start before they actually do,
and can be interspersed with non-indels that start there.
- lines changed 2, context: html, text, full: html, text
Added another test case: first item in primary is an insertion and first item
in secondary is adjacent on the left.
- src/hg/lib/tests/input/annoGrator/insertionsSecondary.vcf
- lines changed 43, context: html, text, full: html, text
Add test cases (and bug fixes!) to make sure that we get the desired
behavior when an insertion is adjacent to a non-insertion, and when
an insertion falls at the start or end of the search region (if applicable):
- Include insertions that fall at the start or end of the search region
- If the primary row is an insertion, keep secondary non-insertion rows
to the left and right.
- If the primary row is a non-insertion, keep secondary insertion rows
at its start and end.
(i.e. keep insertions at boundaries -- but don't let any non-insertions
slip through)
The VCF logic is more complicated because VCF indels always include an
extra base to the left, so they appear to start before they actually do,
and can be interspersed with non-indels that start there.
- lines changed 5, context: html, text, full: html, text
Added another test case: first item in primary is an insertion and first item
in secondary is adjacent on the left.
- lines changed 0, context: html, text, full: html, text
Test & fix VCF+tabix querying of insertion items.
- src/hg/lib/tests/input/annoGrator/insertionsSecondary.vcf.gz
- lines changed 0, context: html, text, full: html, text
Test & fix VCF+tabix querying of insertion items.
- src/hg/lib/tests/input/annoGrator/insertionsSecondary.vcf.gz.tbi
- lines changed 0, context: html, text, full: html, text
Test & fix VCF+tabix querying of insertion items.
- src/hg/lib/web.c
- lines changed 4, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/hg/lib/wikiTrack.c
- lines changed 2, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/hg/makeDb/doc/canFam3.txt
- lines changed 65, context: html, text, full: html, text
lastz runs per Ting lab requests refs #15476
- src/hg/makeDb/doc/hg38/hg38.txt
- src/hg/makeDb/doc/mm10.txt
- src/hg/makeDb/doc/mm9.txt
- lines changed 133, context: html, text, full: html, text
lastz runs per Ting lab requests refs #15476
- src/hg/makeDb/doc/rheMac3.txt
- lines changed 133, context: html, text, full: html, text
lastz runs per Ting lab requests refs #15476
- src/hg/makeDb/doc/rn4.txt
- lines changed 125, context: html, text, full: html, text
lastz runs per Ting lab requests refs #15476
- src/hg/makeDb/outside/gencode/gencodeLoad.mk
- src/hg/makeDb/schema/all.joiner
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 19, context: html, text, full: html, text
Tweak peptideAtlas trackDb (remove supertrack on RR, work-around hgFindspec bug. refs #15998
- lines changed 1, context: html, text, full: html, text
Changing visiblity of track to hide, it was in a superTrack before, and came out to fix a find issue ref# 15998
- src/hg/makeDb/trackDb/human/hg38/trackDb.wgEncode.ra
- src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeSuper.html
- src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV23.html
- src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV23.ra
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 1, context: html, text, full: html, text
changed longLabel of OMIM Genes from Are Disease-causing to Can Be Disease-causing. It always bugged me: the genes themselves are fine, it's only when broken that they cause diesase
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
- src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeSuper.html
- src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM7.html
- src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM7.ra
- lines changed 10, context: html, text, full: html, text
updated mouse GENCODE to have same filters and highlighting as human
- src/hg/mouseStuff/chainToPsl/chainToPsl.c
- lines changed 12, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/hg/mouseStuff/mafCoverage/mafCoverage.c
- lines changed 2, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/hg/pslCDnaFilter/tests/expected/ignoreIntronsTest/drop.psl
- lines changed 1, context: html, text, full: html, text
fixed broken test psl now caught by pslCheck
- src/hg/pslCDnaFilter/tests/expected/noIgnoreIntronsTest/keep.psl
- lines changed 1, context: html, text, full: html, text
fixed broken test psl now caught by pslCheck
- src/hg/pslCDnaFilter/tests/input/ignoreIntrons.psl
- lines changed 1, context: html, text, full: html, text
fixed broken test psl now caught by pslCheck
- src/hg/pslReps/pslReps.c
- lines changed 4, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/hg/utils/automation/genbank/rmskDescription.pl
- lines changed 1, context: html, text, full: html, text
catching up with todays versions refs #16078
- src/hg/utils/gff3ToPsl/tests/expected/grch38ToGrch37Test.psl
- lines changed 18, context: html, text, full: html, text
fixed various problems detected by making pslCheck more stringent
- src/hg/utils/gff3ToPsl/tests/expected/patch1test.psl
- lines changed 264, context: html, text, full: html, text
fixed various problems detected by making pslCheck more stringent
- src/hg/utils/hubCheck/hubCheck.c
- lines changed 1, context: html, text, full: html, text
Initialize var to quiet gcc. refs #16121
- src/hg/utils/otto/decipher/buildDecipher
- lines changed 4, context: html, text, full: html, text
add an index to the decipherRaw file #16107
- src/hg/utils/otto/decipher/makefile
- lines changed 25, context: html, text, full: html, text
add an index to the decipherRaw file #16107
- src/hg/utils/overlapSelect/chromAnnMap.c
- lines changed 1, context: html, text, full: html, text
fixed memory leak that didn't matter
- src/hg/utils/pslMap/pslMap.c
- lines changed 2, context: html, text, full: html, text
fixed various problems detected by making pslCheck more stringent
- src/hg/utils/pslMap/tests/expected/mrnaMapOverChain.mapping.psl
- lines changed 1, context: html, text, full: html, text
fixed various problems detected by making pslCheck more stringent
- src/hg/utils/pslMap/tests/expected/mrnaMapOverSwap.mapping.psl
- lines changed 1, context: html, text, full: html, text
fixed various problems detected by making pslCheck more stringent
- src/hg/utils/pslMap/tests/input/mm6ToHg17.psl
- lines changed 1, context: html, text, full: html, text
fixed various problems detected by making pslCheck more stringent
- src/hg/utils/pslMap/tests/input/retro.psl
- lines changed 4, context: html, text, full: html, text
fixed various problems detected by making pslCheck more stringent
- src/hg/utils/tdbQuery/tdbQuery.c
- lines changed 2, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/inc/psl.h
- lines changed 3, context: html, text, full: html, text
fixed various problems detected by making pslCheck more stringent
- src/jkOwnLib/ffSeedExtend.c
- lines changed 2, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/jkOwnLib/fuzzyFind.c
- lines changed 2, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/jkOwnLib/gfBlatLib.c
- lines changed 2, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/jkOwnLib/xenbig.c
- lines changed 4, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/jkOwnLib/xensmall.c
- lines changed 4, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/lib/annoFormatTab.c
- lines changed 72, context: html, text, full: html, text
On very long queries like selected fields of snp144 chr1 (>11M rows),
hgIntegrator was spending about half of the time repetitively building
up sourceName.columnName strings and looking them up in a hash to tell
whether or not to include each column's data in the output. To avoid
the waste, now it builds up an array (one for each source, primary +
grators) of arrays of flags (one flag for each column) so it can do
an array lookup instead of string-munging and hash lookup.
~2x speedup for selected fields of snp144 chr1 (4 minutes -> 2 minutes).
mysql time is about half that; much of the other half is copying data
in annoStreamDb.c:bufferRowsFromSqlQuery.
- src/lib/annoGrator.c
- lines changed 49, context: html, text, full: html, text
Add test cases (and bug fixes!) to make sure that we get the desired
behavior when an insertion is adjacent to a non-insertion, and when
an insertion falls at the start or end of the search region (if applicable):
- Include insertions that fall at the start or end of the search region
- If the primary row is an insertion, keep secondary non-insertion rows
to the left and right.
- If the primary row is a non-insertion, keep secondary insertion rows
at its start and end.
(i.e. keep insertions at boundaries -- but don't let any non-insertions
slip through)
The VCF logic is more complicated because VCF indels always include an
extra base to the left, so they appear to start before they actually do,
and can be interspersed with non-indels that start there.
- src/lib/annoStreamTab.c
- lines changed 36, context: html, text, full: html, text
Add test cases (and bug fixes!) to make sure that we get the desired
behavior when an insertion is adjacent to a non-insertion, and when
an insertion falls at the start or end of the search region (if applicable):
- Include insertions that fall at the start or end of the search region
- If the primary row is an insertion, keep secondary non-insertion rows
to the left and right.
- If the primary row is a non-insertion, keep secondary insertion rows
at its start and end.
(i.e. keep insertions at boundaries -- but don't let any non-insertions
slip through)
The VCF logic is more complicated because VCF indels always include an
extra base to the left, so they appear to start before they actually do,
and can be interspersed with non-indels that start there.
- src/lib/annoStreamVcf.c
- lines changed 24, context: html, text, full: html, text
Add test cases (and bug fixes!) to make sure that we get the desired
behavior when an insertion is adjacent to a non-insertion, and when
an insertion falls at the start or end of the search region (if applicable):
- Include insertions that fall at the start or end of the search region
- If the primary row is an insertion, keep secondary non-insertion rows
to the left and right.
- If the primary row is a non-insertion, keep secondary insertion rows
at its start and end.
(i.e. keep insertions at boundaries -- but don't let any non-insertions
slip through)
The VCF logic is more complicated because VCF indels always include an
extra base to the left, so they appear to start before they actually do,
and can be interspersed with non-indels that start there.
- lines changed 4, context: html, text, full: html, text
Test & fix VCF+tabix querying of insertion items.
- src/lib/bPlusTree.c
- lines changed 2, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/lib/bbiRead.c
- lines changed 4, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/lib/bbiWrite.c
- lines changed 1, context: html, text, full: html, text
adding limits.h that Braney forgot to add
- src/lib/bigBed.c
- lines changed 9, context: html, text, full: html, text
Add test cases (and bug fixes!) to make sure that we get the desired
behavior when an insertion is adjacent to a non-insertion, and when
an insertion falls at the start or end of the search region (if applicable):
- Include insertions that fall at the start or end of the search region
- If the primary row is an insertion, keep secondary non-insertion rows
to the left and right.
- If the primary row is a non-insertion, keep secondary insertion rows
at its start and end.
(i.e. keep insertions at boundaries -- but don't let any non-insertions
slip through)
The VCF logic is more complicated because VCF indels always include an
extra base to the left, so they appear to start before they actually do,
and can be interspersed with non-indels that start there.
- lines changed 2, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/lib/cheapcgi.c
- lines changed 3, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/lib/codebias.c
- lines changed 2, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/lib/dnautil.c
- lines changed 2, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/lib/fof.c
- lines changed 2, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/lib/mime.c
- lines changed 2, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/lib/net.c
- lines changed 2, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/lib/nt4.c
- lines changed 2, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/lib/options.c
- lines changed 5, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/lib/psl.c
- lines changed 35, context: html, text, full: html, text
fixed various problems detected by making pslCheck more stringent
- src/lib/pslGenoShow.c
- lines changed 10, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/lib/pslShow.c
- lines changed 10, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/lib/udc.c
- lines changed 7, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/lib/wormdna.c
- lines changed 2, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/parasol/para/para.c
- lines changed 4, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/parasol/paraHub/paraHub.c
- lines changed 1, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/parasol/paraNodeStart/paraNodeStart.c
- lines changed 1, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/parasol/parasol/parasol.c
- lines changed 2, context: html, text, full: html, text
fixup gcc warnings for -Wunused-but-set-variable refs #16121
- src/tagStorm/tagStormDeleteTags/delete.tags
- lines changed 3, context: html, text, full: html, text
Added new program tagStormDelete which deletes selected tags from a tagStorm file
- src/tagStorm/tagStormDeleteTags/in.tags
- lines changed 64, context: html, text, full: html, text
Added new program tagStormDelete which deletes selected tags from a tagStorm file
- src/tagStorm/tagStormDeleteTags/makefile
- lines changed 3, context: html, text, full: html, text
Added new program tagStormDelete which deletes selected tags from a tagStorm file
- src/tagStorm/tagStormDeleteTags/out.tags
- lines changed 53, context: html, text, full: html, text
Added new program tagStormDelete which deletes selected tags from a tagStorm file
- src/tagStorm/tagStormDeleteTags/tagStormDeleteTags.c
- lines changed 76, context: html, text, full: html, text
Added new program tagStormDelete which deletes selected tags from a tagStorm file
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed 3, context: html, text, full: html, text
v323 final build refs #16092
- lines changed: 3681
- files changed: 136