All File Changes
v297_preview2 to v297_base (2014-03-10 to 2014-03-17) v297
- src/hg/cartDump/cartDump.c
- lines changed 4, context: html, text, full: html, text
Adding bottleneck delay call to cartDump to discourage hackers from abusing cartDump to snoop on carts.
- src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeEncode2Submit/edwFakeEncode2Submit.c
- lines changed 95, context: html, text, full: html, text
dd code to do handle the discrepancy between mdbQuery outputand actual encode2 files imported into encodeDataWarehouse.
- src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwUserTable/rsyncEdwUserTable.c
- lines changed 87, context: html, text, full: html, text
Update edwUser table using user information from encodedcc.encodedcc has changed the REST API to use uuid instead of
email address to identify a user.
- src/hg/encode3/validateManifest/VERSION.TXT
- src/hg/hgBlat/hgBlat.c
- lines changed 12, context: html, text, full: html, text
Moving code from commit 0fb6cafc5cebeb0f383804ed9df2cd01be10227f into hdbbecause it's also needed by hgPcr. refs #11957. (Should not affect RR, as
hReplaceGbdb will return the same string, so it only adds and then
removes a .2bit filename from the path.)
- src/hg/hgCustom/hgCustom.c
- lines changed 4, context: html, text, full: html, text
In code review, Max pointed out that it's non-standard to conditionallyinclude header files in the middle of a .c file. While looking at it,
I realized that there were a lot of unnecessary #ifdef's for KNETFILE_HOOKS
in general, all because there was not yet an #else implementation of
knetUdcInstall, which can be a no-op if KNETFILE_HOOKS is not used.
So I yanked out a lot of unnecessary old stuff, and tested basic bam and
vcf track operations with a few settings:
USE_SAMTABIX USE_BAM USE_TABIX KNETFILE_HOOKS
1 (these tree are all implied by USE_SAMTABIX)
0 1 0 0
0 1 0 1
0 0 1 1
USE_TABIX without KNETFILE_HOOKS doesn't work because the tabix lib
wants to download .tbi files into the current working directory,
cgi-bin, and we don't allow that (and shouldn't!). If we were going
to support that, we could add a change-dir solution as in bamFile.c,
but I don't think we need to support it now that there's samtabix.
refs #6235, refs #12850
- src/hg/hgMirror/hgMirror
- lines changed 248, context: html, text, full: html, text
adding clade/org/db options like on hgGateway to hgMirror, refs #11957
- lines changed 1, context: html, text, full: html, text
suppress email message from test at job, refs #11957
- src/hg/hgPcr/hgPcr.c
- lines changed 1, context: html, text, full: html, text
Moving code from commit 0fb6cafc5cebeb0f383804ed9df2cd01be10227f into hdbbecause it's also needed by hgPcr. refs #11957. (Should not affect RR, as
hReplaceGbdb will return the same string, so it only adds and then
removes a .2bit filename from the path.)
- src/hg/hgSession/hgSession.c
- lines changed 1, context: html, text, full: html, text
oops another missed type change for hgsid in hgSession
- src/hg/hgTables/bam.c
- lines changed 5, context: html, text, full: html, text
In code review, Max pointed out that it's non-standard to conditionallyinclude header files in the middle of a .c file. While looking at it,
I realized that there were a lot of unnecessary #ifdef's for KNETFILE_HOOKS
in general, all because there was not yet an #else implementation of
knetUdcInstall, which can be a no-op if KNETFILE_HOOKS is not used.
So I yanked out a lot of unnecessary old stuff, and tested basic bam and
vcf track operations with a few settings:
USE_SAMTABIX USE_BAM USE_TABIX KNETFILE_HOOKS
1 (these tree are all implied by USE_SAMTABIX)
0 1 0 0
0 1 0 1
0 0 1 1
USE_TABIX without KNETFILE_HOOKS doesn't work because the tabix lib
wants to download .tbi files into the current working directory,
cgi-bin, and we don't allow that (and shouldn't!). If we were going
to support that, we could add a change-dir solution as in bamFile.c,
but I don't think we need to support it now that there's samtabix.
refs #6235, refs #12850
- src/hg/hgTables/hgTables.c
- lines changed 4, context: html, text, full: html, text
In code review, Max pointed out that it's non-standard to conditionallyinclude header files in the middle of a .c file. While looking at it,
I realized that there were a lot of unnecessary #ifdef's for KNETFILE_HOOKS
in general, all because there was not yet an #else implementation of
knetUdcInstall, which can be a no-op if KNETFILE_HOOKS is not used.
So I yanked out a lot of unnecessary old stuff, and tested basic bam and
vcf track operations with a few settings:
USE_SAMTABIX USE_BAM USE_TABIX KNETFILE_HOOKS
1 (these tree are all implied by USE_SAMTABIX)
0 1 0 0
0 1 0 1
0 0 1 1
USE_TABIX without KNETFILE_HOOKS doesn't work because the tabix lib
wants to download .tbi files into the current working directory,
cgi-bin, and we don't allow that (and shouldn't!). If we were going
to support that, we could add a change-dir solution as in bamFile.c,
but I don't think we need to support it now that there's samtabix.
refs #6235, refs #12850
- src/hg/hgTables/vcf.c
- lines changed 5, context: html, text, full: html, text
In code review, Max pointed out that it's non-standard to conditionallyinclude header files in the middle of a .c file. While looking at it,
I realized that there were a lot of unnecessary #ifdef's for KNETFILE_HOOKS
in general, all because there was not yet an #else implementation of
knetUdcInstall, which can be a no-op if KNETFILE_HOOKS is not used.
So I yanked out a lot of unnecessary old stuff, and tested basic bam and
vcf track operations with a few settings:
USE_SAMTABIX USE_BAM USE_TABIX KNETFILE_HOOKS
1 (these tree are all implied by USE_SAMTABIX)
0 1 0 0
0 1 0 1
0 0 1 1
USE_TABIX without KNETFILE_HOOKS doesn't work because the tabix lib
wants to download .tbi files into the current working directory,
cgi-bin, and we don't allow that (and shouldn't!). If we were going
to support that, we could add a change-dir solution as in bamFile.c,
but I don't think we need to support it now that there's samtabix.
refs #6235, refs #12850
- src/hg/hgTracks/bamTrack.c
- lines changed 4, context: html, text, full: html, text
In code review, Max pointed out that it's non-standard to conditionallyinclude header files in the middle of a .c file. While looking at it,
I realized that there were a lot of unnecessary #ifdef's for KNETFILE_HOOKS
in general, all because there was not yet an #else implementation of
knetUdcInstall, which can be a no-op if KNETFILE_HOOKS is not used.
So I yanked out a lot of unnecessary old stuff, and tested basic bam and
vcf track operations with a few settings:
USE_SAMTABIX USE_BAM USE_TABIX KNETFILE_HOOKS
1 (these tree are all implied by USE_SAMTABIX)
0 1 0 0
0 1 0 1
0 0 1 1
USE_TABIX without KNETFILE_HOOKS doesn't work because the tabix lib
wants to download .tbi files into the current working directory,
cgi-bin, and we don't allow that (and shouldn't!). If we were going
to support that, we could add a change-dir solution as in bamFile.c,
but I don't think we need to support it now that there's samtabix.
refs #6235, refs #12850
- src/hg/hgTracks/hgTracks.c
- lines changed 9, context: html, text, full: html, text
added a 100X zoom-out button. working with Jonathan. refs #7475
- src/hg/hgTracks/loweLabTracks.c
- lines changed 7, context: html, text, full: html, text
fixup logic and compile problems for Mac OSX refs #12209
- src/hg/hgTracks/vcfTrack.c
- lines changed 10, context: html, text, full: html, text
In code review, Max pointed out that it's non-standard to conditionallyinclude header files in the middle of a .c file. While looking at it,
I realized that there were a lot of unnecessary #ifdef's for KNETFILE_HOOKS
in general, all because there was not yet an #else implementation of
knetUdcInstall, which can be a no-op if KNETFILE_HOOKS is not used.
So I yanked out a lot of unnecessary old stuff, and tested basic bam and
vcf track operations with a few settings:
USE_SAMTABIX USE_BAM USE_TABIX KNETFILE_HOOKS
1 (these tree are all implied by USE_SAMTABIX)
0 1 0 0
0 1 0 1
0 0 1 1
USE_TABIX without KNETFILE_HOOKS doesn't work because the tabix lib
wants to download .tbi files into the current working directory,
cgi-bin, and we don't allow that (and shouldn't!). If we were going
to support that, we could add a change-dir solution as in bamFile.c,
but I don't think we need to support it now that there's samtabix.
refs #6235, refs #12850
- src/hg/hgVai/hgVai.c
- lines changed 2, context: html, text, full: html, text
In code review, Max pointed out that it's non-standard to conditionallyinclude header files in the middle of a .c file. While looking at it,
I realized that there were a lot of unnecessary #ifdef's for KNETFILE_HOOKS
in general, all because there was not yet an #else implementation of
knetUdcInstall, which can be a no-op if KNETFILE_HOOKS is not used.
So I yanked out a lot of unnecessary old stuff, and tested basic bam and
vcf track operations with a few settings:
USE_SAMTABIX USE_BAM USE_TABIX KNETFILE_HOOKS
1 (these tree are all implied by USE_SAMTABIX)
0 1 0 0
0 1 0 1
0 0 1 1
USE_TABIX without KNETFILE_HOOKS doesn't work because the tabix lib
wants to download .tbi files into the current working directory,
cgi-bin, and we don't allow that (and shouldn't!). If we were going
to support that, we could add a change-dir solution as in bamFile.c,
but I don't think we need to support it now that there's samtabix.
refs #6235, refs #12850
- src/hg/hgVai/libifyMe.c
- lines changed 1, context: html, text, full: html, text
Fixing problem with hgVai code not recognizing a genePred whoseasObject was derived from sql field info. Unfortunately, when a sql
field's type is longblob, we don't know whether its autoSql definition
was a list (like exonStarts[exonCount]) or just an lstring. To play
it safe, we call it an lstring which works fine for feeding data
through the annoGrator system. However, when comparing a sql-derived
asObj with lstring to the real autoSql-derived asObj, asCompareObjs
will see different types for the same field and return false. So
for the purposes of recognizing a genePred, we need to simply compare
column names.
- src/hg/hgVarAnnogrator/hgVarAnnogrator.c
- lines changed 2, context: html, text, full: html, text
Fixing problem with hgVai code not recognizing a genePred whoseasObject was derived from sql field info. Unfortunately, when a sql
field's type is longblob, we don't know whether its autoSql definition
was a list (like exonStarts[exonCount]) or just an lstring. To play
it safe, we call it an lstring which works fine for feeding data
through the annoGrator system. However, when comparing a sql-derived
asObj with lstring to the real autoSql-derived asObj, asCompareObjs
will see different types for the same field and return false. So
for the purposes of recognizing a genePred, we need to simply compare
column names.
- lines changed 4, context: html, text, full: html, text
In code review, Max pointed out that it's non-standard to conditionallyinclude header files in the middle of a .c file. While looking at it,
I realized that there were a lot of unnecessary #ifdef's for KNETFILE_HOOKS
in general, all because there was not yet an #else implementation of
knetUdcInstall, which can be a no-op if KNETFILE_HOOKS is not used.
So I yanked out a lot of unnecessary old stuff, and tested basic bam and
vcf track operations with a few settings:
USE_SAMTABIX USE_BAM USE_TABIX KNETFILE_HOOKS
1 (these tree are all implied by USE_SAMTABIX)
0 1 0 0
0 1 0 1
0 0 1 1
USE_TABIX without KNETFILE_HOOKS doesn't work because the tabix lib
wants to download .tbi files into the current working directory,
cgi-bin, and we don't allow that (and shouldn't!). If we were going
to support that, we could add a change-dir solution as in bamFile.c,
but I don't think we need to support it now that there's samtabix.
refs #6235, refs #12850
- src/hg/hgc/bamClick.c
- lines changed 4, context: html, text, full: html, text
In code review, Max pointed out that it's non-standard to conditionallyinclude header files in the middle of a .c file. While looking at it,
I realized that there were a lot of unnecessary #ifdef's for KNETFILE_HOOKS
in general, all because there was not yet an #else implementation of
knetUdcInstall, which can be a no-op if KNETFILE_HOOKS is not used.
So I yanked out a lot of unnecessary old stuff, and tested basic bam and
vcf track operations with a few settings:
USE_SAMTABIX USE_BAM USE_TABIX KNETFILE_HOOKS
1 (these tree are all implied by USE_SAMTABIX)
0 1 0 0
0 1 0 1
0 0 1 1
USE_TABIX without KNETFILE_HOOKS doesn't work because the tabix lib
wants to download .tbi files into the current working directory,
cgi-bin, and we don't allow that (and shouldn't!). If we were going
to support that, we could add a change-dir solution as in bamFile.c,
but I don't think we need to support it now that there's samtabix.
refs #6235, refs #12850
- src/hg/hgc/vcfClick.c
- lines changed 9, context: html, text, full: html, text
In code review, Max pointed out that it's non-standard to conditionallyinclude header files in the middle of a .c file. While looking at it,
I realized that there were a lot of unnecessary #ifdef's for KNETFILE_HOOKS
in general, all because there was not yet an #else implementation of
knetUdcInstall, which can be a no-op if KNETFILE_HOOKS is not used.
So I yanked out a lot of unnecessary old stuff, and tested basic bam and
vcf track operations with a few settings:
USE_SAMTABIX USE_BAM USE_TABIX KNETFILE_HOOKS
1 (these tree are all implied by USE_SAMTABIX)
0 1 0 0
0 1 0 1
0 0 1 1
USE_TABIX without KNETFILE_HOOKS doesn't work because the tabix lib
wants to download .tbi files into the current working directory,
cgi-bin, and we don't allow that (and shouldn't!). If we were going
to support that, we could add a change-dir solution as in bamFile.c,
but I don't think we need to support it now that there's samtabix.
refs #6235, refs #12850
- src/hg/htdocs/ENCODE/pubsEncode.html
- lines changed 5022, context: html, text, full: html, text
Overhaul/addition of publications to ENCODED-funded pubs page/Mike Pazin refs# 12863
- src/hg/htdocs/ENCODE/pubsOther.html
- lines changed 3, context: html, text, full: html, text
Small edits, corrections to pubsOther.html for ENCODE update from Mike Pazin, refs# 12863
- src/hg/htdocs/contacts.html
- lines changed 9, context: html, text, full: html, text
Adding section about with link to training per bob and Donna's comments.
- src/hg/htdocs/goldenPath/help/customTrackText.html
- lines changed 1, context: html, text, full: html, text
Added missing colon, refs #12849
- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
- lines changed 33, context: html, text, full: html, text
Adding highlights/links to My Hubs tab to encourage pasting hub.txt there before building URLs. Adding notes about building URLs in sessions section. refs# 12696
- lines changed 1, context: html, text, full: html, text
Small change to hgTrackHubHelp.html refs# 12696
- src/hg/htdocs/goldenPath/newsarch.html
- lines changed 1, context: html, text, full: html, text
Changing 'survey' to 'signup' per bob's request.
- src/hg/htdocs/inc/globalNavBar.inc
- lines changed 2, context: html, text, full: html, text
changed menuparent tag =last= to About Us link, per Jonathan. refs #12853
- src/hg/htdocs/style/nice_menu.css
- lines changed 1, context: html, text, full: html, text
Added a comment as requested by Kate in code review.
- src/hg/htdocs/training.html
- lines changed 1, context: html, text, full: html, text
Changing 'survey' to 'signup' per bob's request.
- src/hg/inc/hdb.h
- lines changed 4, context: html, text, full: html, text
Moving code from commit 0fb6cafc5cebeb0f383804ed9df2cd01be10227f into hdbbecause it's also needed by hgPcr. refs #11957. (Should not affect RR, as
hReplaceGbdb will return the same string, so it only adds and then
removes a .2bit filename from the path.)
- src/hg/inc/hui.h
- lines changed 1, context: html, text, full: html, text
added a 100X zoom-out button. working with Jonathan. refs #7475
- src/hg/inc/versionInfo.h
- src/hg/lib/annoFormatVep.c
- lines changed 1, context: html, text, full: html, text
Fixing problem with hgVai code not recognizing a genePred whoseasObject was derived from sql field info. Unfortunately, when a sql
field's type is longblob, we don't know whether its autoSql definition
was a list (like exonStarts[exonCount]) or just an lstring. To play
it safe, we call it an lstring which works fine for feeding data
through the annoGrator system. However, when comparing a sql-derived
asObj with lstring to the real autoSql-derived asObj, asCompareObjs
will see different types for the same field and return false. So
for the purposes of recognizing a genePred, we need to simply compare
column names.
- src/hg/lib/customFactory.c
- lines changed 2, context: html, text, full: html, text
customFactory for bedDetails still needs to pass in the SQL file.
- src/hg/lib/customPp.c
- lines changed 15, context: html, text, full: html, text
Tweaking bigUrlToTrackLine to handle ".vcf.gz" which has two file extensions.
- src/hg/lib/hdb.c
- lines changed 21, context: html, text, full: html, text
Moving code from commit 0fb6cafc5cebeb0f383804ed9df2cd01be10227f into hdbbecause it's also needed by hgPcr. refs #11957. (Should not affect RR, as
hReplaceGbdb will return the same string, so it only adds and then
removes a .2bit filename from the path.)
- lines changed 2, context: html, text, full: html, text
change of comment after refs #12849
- src/hg/lib/hui.c
- lines changed 1, context: html, text, full: html, text
added a 100X zoom-out button. working with Jonathan. refs #7475
- src/hg/lib/jksql.c
- lines changed 63, context: html, text, full: html, text
after code review: changed comments and variable names in jksql.Only aesthestics, no logic change in this commit.
Should make the code more readable. refs #12849
- src/hg/lib/spOldNew.sql
- lines changed 1, context: html, text, full: html, text
mm10 ucsc genes is ready for QA, reloading uniProt table to fix bug inspToDb. Load a coupple more tables in the proteome database
- src/hg/lib/spVariant.sql
- lines changed 1, context: html, text, full: html, text
mm10 ucsc genes is ready for QA, reloading uniProt table to fix bug inspToDb. Load a coupple more tables in the proteome database
- src/hg/lib/tests/annoGratorTester.c
- lines changed 1, context: html, text, full: html, text
Fixing problem with hgVai code not recognizing a genePred whoseasObject was derived from sql field info. Unfortunately, when a sql
field's type is longblob, we don't know whether its autoSql definition
was a list (like exonStarts[exonCount]) or just an lstring. To play
it safe, we call it an lstring which works fine for feeding data
through the annoGrator system. However, when comparing a sql-derived
asObj with lstring to the real autoSql-derived asObj, asCompareObjs
will see different types for the same field and return false. So
for the purposes of recognizing a genePred, we need to simply compare
column names.
- lines changed 6, context: html, text, full: html, text
In code review, Max pointed out that it's non-standard to conditionallyinclude header files in the middle of a .c file. While looking at it,
I realized that there were a lot of unnecessary #ifdef's for KNETFILE_HOOKS
in general, all because there was not yet an #else implementation of
knetUdcInstall, which can be a no-op if KNETFILE_HOOKS is not used.
So I yanked out a lot of unnecessary old stuff, and tested basic bam and
vcf track operations with a few settings:
USE_SAMTABIX USE_BAM USE_TABIX KNETFILE_HOOKS
1 (these tree are all implied by USE_SAMTABIX)
0 1 0 0
0 1 0 1
0 0 1 1
USE_TABIX without KNETFILE_HOOKS doesn't work because the tabix lib
wants to download .tbi files into the current working directory,
cgi-bin, and we don't allow that (and shouldn't!). If we were going
to support that, we could add a change-dir solution as in bamFile.c,
but I don't think we need to support it now that there's samtabix.
refs #6235, refs #12850
- src/hg/lib/vcfUi.c
- lines changed 4, context: html, text, full: html, text
In code review, Max pointed out that it's non-standard to conditionallyinclude header files in the middle of a .c file. While looking at it,
I realized that there were a lot of unnecessary #ifdef's for KNETFILE_HOOKS
in general, all because there was not yet an #else implementation of
knetUdcInstall, which can be a no-op if KNETFILE_HOOKS is not used.
So I yanked out a lot of unnecessary old stuff, and tested basic bam and
vcf track operations with a few settings:
USE_SAMTABIX USE_BAM USE_TABIX KNETFILE_HOOKS
1 (these tree are all implied by USE_SAMTABIX)
0 1 0 0
0 1 0 1
0 0 1 1
USE_TABIX without KNETFILE_HOOKS doesn't work because the tabix lib
wants to download .tbi files into the current working directory,
cgi-bin, and we don't allow that (and shouldn't!). If we were going
to support that, we could add a change-dir solution as in bamFile.c,
but I don't think we need to support it now that there's samtabix.
refs #6235, refs #12850
- src/hg/makeDb/doc/encodeRegHg19.txt
- lines changed 5, context: html, text, full: html, text
Update to Factorbook motif info.
- lines changed 17, context: html, text, full: html, text
A few corrections to canonical motif table, from Factorbook team. Note table rename. refs #12551
- src/hg/makeDb/doc/makeEnsembl.txt
- lines changed 1278, context: html, text, full: html, text
record procedures for v75 update refs #12796
- src/hg/makeDb/doc/proteins/140122.txt
- lines changed 37, context: html, text, full: html, text
mm10 ucsc genes is ready for QA, reloading uniProt table to fix bug inspToDb. Load a coupple more tables in the proteome database
- src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes14.csh
- lines changed 258, context: html, text, full: html, text
mm10 ucsc genes is ready for QA, reloading uniProt table to fix bug inspToDb. Load a coupple more tables in the proteome database
- src/hg/makeDb/doc/uniProt/sp140122.txt
- lines changed 35, context: html, text, full: html, text
mm10 ucsc genes is ready for QA, reloading uniProt table to fix bug inspToDb. Load a coupple more tables in the proteome database
- src/hg/makeDb/schema/all.joiner
- lines changed 1, context: html, text, full: html, text
Fixed an error (redmine #12639)
- lines changed 1, context: html, text, full: html, text
disable kg5ToKg6 checking on mm10 with new gene set
- lines changed 6, context: html, text, full: html, text
Making small all.joiner changes to remove dup error, minCheck error for new motif track refs# 12551
- src/hg/makeDb/trackDb/anopheles/anoGam1/description.html
- lines changed 3, context: html, text, full: html, text
Fixing links on anoGam1 track description pages
- src/hg/makeDb/trackDb/anopheles/est.html
- lines changed 14, context: html, text, full: html, text
Fixing links on anoGam1 track description pages
- src/hg/makeDb/trackDb/anopheles/intronEst.html
- lines changed 14, context: html, text, full: html, text
Fixing links on anoGam1 track description pages
- src/hg/makeDb/trackDb/anopheles/mrna.html
- lines changed 14, context: html, text, full: html, text
Fixing links on anoGam1 track description pages
- src/hg/makeDb/trackDb/anopheles/rmsk.html
- lines changed 5, context: html, text, full: html, text
Fixing links on anoGam1 track description pages
- src/hg/makeDb/trackDb/anopheles/xenoMrna.html
- lines changed 14, context: html, text, full: html, text
Fixing links on anoGam1 track description pages
- src/hg/makeDb/trackDb/bushbaby/otoGar3/description.html
- lines changed 2, context: html, text, full: html, text
Fixing links on bushBaby (otoGar3), gator (allMis1), and worm (caePb2) track description pages
- src/hg/makeDb/trackDb/bushbaby/otoGar3/gap.html
- lines changed 1, context: html, text, full: html, text
Fixing links on bushBaby (otoGar3), gator (allMis1), and worm (caePb2) track description pages
- src/hg/makeDb/trackDb/bushbaby/otoGar3/gold.html
- lines changed 1, context: html, text, full: html, text
Fixing links on bushBaby (otoGar3), gator (allMis1), and worm (caePb2) track description pages
- src/hg/makeDb/trackDb/gator/allMis1/description.html
- lines changed 2, context: html, text, full: html, text
Fixing links on bushBaby (otoGar3), gator (allMis1), and worm (caePb2) track description pages
- src/hg/makeDb/trackDb/gator/allMis1/gap.html
- lines changed 1, context: html, text, full: html, text
Fixing links on bushBaby (otoGar3), gator (allMis1), and worm (caePb2) track description pages
- src/hg/makeDb/trackDb/gator/allMis1/gold.html
- lines changed 1, context: html, text, full: html, text
Fixing links on bushBaby (otoGar3), gator (allMis1), and worm (caePb2) track description pages
- src/hg/makeDb/trackDb/human/hg18/defaultPriority.ra
- lines changed 18, context: html, text, full: html, text
reorder hg18 to the new default ordering refs #7343
- src/hg/makeDb/trackDb/human/hg18/trackDb.ra
- lines changed 119, context: html, text, full: html, text
reorder hg18 to the new default ordering refs #7343
- src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
- lines changed 2, context: html, text, full: html, text
reorder hg18 to the new default ordering refs #7343
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 1, context: html, text, full: html, text
Fixed capitalization of RefSeq in a long label. RM #12851.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgSegmentation.html
- lines changed 71, context: html, text, full: html, text
Fixes to trackDb and updates to track description based on input from contributors (Hoffman, Wilder). refs #12259
- src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgSegmentation.ra
- lines changed 3, context: html, text, full: html, text
Fixes to trackDb and updates to track description based on input from contributors (Hoffman, Wilder). refs #12259
- src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
- lines changed 188, context: html, text, full: html, text
A few corrections to canonical motif table, from Factorbook team. Note table rename. refs #12551
- lines changed 189, context: html, text, full: html, text
Removing beta TfbsClusteredV3 that used motifsV2 table, set dev entry to alpha,beta and from dense to hide ref# 12551
- lines changed 19, context: html, text, full: html, text
Removing public V3 Tfbs stanza, replacing with V4/wgEncodeRegTfbsClusteredV3 track, setting to non-default display refs# 12551
- lines changed 1, context: html, text, full: html, text
Removing release lines from wgEncodeRegTfbsClusteredV3/V4 to make it public refs# 12551
- src/hg/makeDb/trackDb/human/hg38/altSequence.html
- lines changed 1, context: html, text, full: html, text
Fixed an html tag (redmine #12851)
- src/hg/makeDb/trackDb/human/hg38/description.html
- lines changed 1, context: html, text, full: html, text
Fixed a typo (redmine #12851)
- lines changed 3, context: html, text, full: html, text
Added link to GRC assembly terms definitions, per RM #12851.
- src/hg/makeDb/trackDb/human/hg38/knownGene.html
- lines changed 163, context: html, text, full: html, text
add updated knownGene.html page for hg38. This will probably need acouple more tweaks to get the numbers right for non-coding, etc
- src/hg/makeDb/trackDb/human/placentalChainNet.html
- lines changed 2, context: html, text, full: html, text
the date/db construct is now redundant since date includes db refs #12864
- src/hg/makeDb/trackDb/human/primateChainNet.html
- lines changed 2, context: html, text, full: html, text
the date/db construct is now redundant since date includes db refs #12864
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 9, context: html, text, full: html, text
Adding a catch-all LRG transcript search as Steve suggested in #12882.Searching for "LRG_321" still won't get the LRG Regions item, but it
will get all transcripts (LRG_321t*) in the LRG Transcripts track.
refs #12882
- lines changed 40, context: html, text, full: html, text
Fixed capitalization inconsistencies in long labels.
- src/hg/makeDb/trackDb/human/vertebrateChainNet.html
- lines changed 2, context: html, text, full: html, text
the date/db construct is now redundant since date includes db refs #12864
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
- lines changed 20, context: html, text, full: html, text
add knownGeneOld6 to trackDb for Old UCSC Genes track.
- src/hg/makeDb/trackDb/trackDb.ra
- lines changed 16, context: html, text, full: html, text
Fixed capitalization inconsistencies in long labels.
- src/hg/makeDb/trackDb/worm/caePb2/ctgPos2.html
- lines changed 2, context: html, text, full: html, text
Fixing links on bushBaby (otoGar3), gator (allMis1), and worm (caePb2) track description pages
- src/hg/makeDb/trackDb/worm/caePb2/description.html
- lines changed 4, context: html, text, full: html, text
Fixing links on bushBaby (otoGar3), gator (allMis1), and worm (caePb2) track description pages
- src/hg/makeDb/trackDb/worm/caePb2/gap.html
- lines changed 2, context: html, text, full: html, text
Fixing links on bushBaby (otoGar3), gator (allMis1), and worm (caePb2) track description pages
- src/hg/makeDb/trackDb/worm/caePb2/gold.html
- lines changed 2, context: html, text, full: html, text
Fixing links on bushBaby (otoGar3), gator (allMis1), and worm (caePb2) track description pages
- src/hg/protein/spToDb/spToDb.c
- lines changed 1, context: html, text, full: html, text
mm10 ucsc genes is ready for QA, reloading uniProt table to fix bug inspToDb. Load a coupple more tables in the proteome database
- src/hg/ratStuff/mafAddQRows/mafAddQRows.c
- lines changed 2, context: html, text, full: html, text
correcting mafAddQRows logic and compile error refs @12209
- src/hg/utils/automation/doEnsGeneUpdate.pl
- lines changed 1, context: html, text, full: html, text
do not want to use name2 as gene name refs #12796
- src/hg/utils/makeTableList/makeTableList.c
- lines changed 89, context: html, text, full: html, text
changing makeTableList command for better compatibility with Jorge'scronjobs, refs #11957
- src/inc/asParse.h
- lines changed 11, context: html, text, full: html, text
Fixing problem with hgVai code not recognizing a genePred whoseasObject was derived from sql field info. Unfortunately, when a sql
field's type is longblob, we don't know whether its autoSql definition
was a list (like exonStarts[exonCount]) or just an lstring. To play
it safe, we call it an lstring which works fine for feeding data
through the annoGrator system. However, when comparing a sql-derived
asObj with lstring to the real autoSql-derived asObj, asCompareObjs
will see different types for the same field and return false. So
for the purposes of recognizing a genePred, we need to simply compare
column names.
- src/inc/bigWig.h
- lines changed 11, context: html, text, full: html, text
fix an issue with a function definition change that was breaking BioPerl
- src/inc/userApp.mk
- lines changed 1, context: html, text, full: html, text
correcting mafAddQRows logic and compile error refs @12209
- src/lib/asParse.c
- lines changed 41, context: html, text, full: html, text
Fixing problem with hgVai code not recognizing a genePred whoseasObject was derived from sql field info. Unfortunately, when a sql
field's type is longblob, we don't know whether its autoSql definition
was a list (like exonStarts[exonCount]) or just an lstring. To play
it safe, we call it an lstring which works fine for feeding data
through the annoGrator system. However, when comparing a sql-derived
asObj with lstring to the real autoSql-derived asObj, asCompareObjs
will see different types for the same field and return false. So
for the purposes of recognizing a genePred, we need to simply compare
column names.
- src/lib/bamFile.c
- lines changed 25, context: html, text, full: html, text
In code review, Max pointed out that it's non-standard to conditionallyinclude header files in the middle of a .c file. While looking at it,
I realized that there were a lot of unnecessary #ifdef's for KNETFILE_HOOKS
in general, all because there was not yet an #else implementation of
knetUdcInstall, which can be a no-op if KNETFILE_HOOKS is not used.
So I yanked out a lot of unnecessary old stuff, and tested basic bam and
vcf track operations with a few settings:
USE_SAMTABIX USE_BAM USE_TABIX KNETFILE_HOOKS
1 (these tree are all implied by USE_SAMTABIX)
0 1 0 0
0 1 0 1
0 0 1 1
USE_TABIX without KNETFILE_HOOKS doesn't work because the tabix lib
wants to download .tbi files into the current working directory,
cgi-bin, and we don't allow that (and shouldn't!). If we were going
to support that, we could add a change-dir solution as in bamFile.c,
but I don't think we need to support it now that there's samtabix.
refs #6235, refs #12850
- src/lib/bwgCreate.c
- lines changed 16, context: html, text, full: html, text
fix an issue with a function definition change that was breaking BioPerl
- src/lib/knetUdc.c
- lines changed 9, context: html, text, full: html, text
In code review, Max pointed out that it's non-standard to conditionallyinclude header files in the middle of a .c file. While looking at it,
I realized that there were a lot of unnecessary #ifdef's for KNETFILE_HOOKS
in general, all because there was not yet an #else implementation of
knetUdcInstall, which can be a no-op if KNETFILE_HOOKS is not used.
So I yanked out a lot of unnecessary old stuff, and tested basic bam and
vcf track operations with a few settings:
USE_SAMTABIX USE_BAM USE_TABIX KNETFILE_HOOKS
1 (these tree are all implied by USE_SAMTABIX)
0 1 0 0
0 1 0 1
0 0 1 1
USE_TABIX without KNETFILE_HOOKS doesn't work because the tabix lib
wants to download .tbi files into the current working directory,
cgi-bin, and we don't allow that (and shouldn't!). If we were going
to support that, we could add a change-dir solution as in bamFile.c,
but I don't think we need to support it now that there's samtabix.
refs #6235, refs #12850
- src/lib/linefile.c
- lines changed 5, context: html, text, full: html, text
minor: use stack instead of needMem for temporary string.
- lines changed 5, context: html, text, full: html, text
In code review, Max pointed out that it's non-standard to conditionallyinclude header files in the middle of a .c file. While looking at it,
I realized that there were a lot of unnecessary #ifdef's for KNETFILE_HOOKS
in general, all because there was not yet an #else implementation of
knetUdcInstall, which can be a no-op if KNETFILE_HOOKS is not used.
So I yanked out a lot of unnecessary old stuff, and tested basic bam and
vcf track operations with a few settings:
USE_SAMTABIX USE_BAM USE_TABIX KNETFILE_HOOKS
1 (these tree are all implied by USE_SAMTABIX)
0 1 0 0
0 1 0 1
0 0 1 1
USE_TABIX without KNETFILE_HOOKS doesn't work because the tabix lib
wants to download .tbi files into the current working directory,
cgi-bin, and we don't allow that (and shouldn't!). If we were going
to support that, we could add a change-dir solution as in bamFile.c,
but I don't think we need to support it now that there's samtabix.
refs #6235, refs #12850
- src/product/README.install
- lines changed 8, context: html, text, full: html, text
add note about Options +Includes refs #252
- lines changed 1, context: html, text, full: html, text
add note about Options +Includes refs #252
- src/product/scripts/trashSizeMonitor.sh
- lines changed 3, context: html, text, full: html, text
need trash to measure trash does not work on empty trash refs #11957
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed 3, context: html, text, full: html, text
v297 final build refs #12656
- src/utils/wigToBigWig/wigToBigWig.c
- lines changed 1, context: html, text, full: html, text
fix an issue with a function definition change that was breaking BioPerl
- lines changed: 8542
- files changed: 113