All File Changes

v282_preview2 to v282_base (2013-04-09 to 2013-04-16) v282

• src/blatz/makefile
  • lines changed 6, context: html, text, full: html, text
    correctly using DESTDIR with BINDIR refs #9104
• src/hg/altSplice/altSplice/tests/makefile
  • lines changed 9, context: html, text, full: html, text
    eliminate BINDIR from tests makefile, refs #9104
• src/hg/bedIntersect/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    eliminate BINDIR from tests makefile, refs #9104
• src/hg/bedItemOverlapCount/tests/makefile
  • lines changed 3, context: html, text, full: html, text
    add makefile for running tests refs #9104
  • lines changed 3, context: html, text, full: html, text
    add clean target to satisify that from the call above refs #9104
• src/hg/blastToPsl/tests/makefile
  • lines changed 4, context: html, text, full: html, text
    eliminate BINDIR from tests makefile, refs #9104
• src/hg/checkTableCoords/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    do not use BINDIR in the tests makefile to reference the test program
• src/hg/chimpStuff/chimpChromContigAgp/tests/makefile
  • lines changed 2, context: html, text, full: html, text
    eliminate BINDIR from tests makefile, refs #9104
• src/hg/encode/regionAgp/tests/makefile
  • lines changed 7, context: html, text, full: html, text
    eliminate BINDIR from tests makefile, refs #9104
• src/hg/encode3/encodeDataWarehouse/edwAddAssembly/edwAddAssembly.c
  • lines changed 65, context: html, text, full: html, text
    Added new assembly loader for encode data warehouse
  • lines changed 5, context: html, text, full: html, text
    Polishing bits of schema to do with encodeQa, and refactoring for qa pipeline.
  • lines changed 18, context: html, text, full: html, text
    Implementing a number of Stanford's suggestions including not assigning license plate until later (which means files need another name before validation), and changing what internally used files are plated and what are not. Now submission files are not plated, but files used in QA pipeline are
• src/hg/encode3/encodeDataWarehouse/edwAddAssembly/makefile
  • lines changed 4, context: html, text, full: html, text
    Added new assembly loader for encode data warehouse
• src/hg/encode3/encodeDataWarehouse/edwAddQaEnrichTarget/edwAddQaEnrichTarget.c
  • lines changed 94, context: html, text, full: html, text
    Program to load a new enrichment target bed to database.
  • lines changed 39, context: html, text, full: html, text
    Implementing a number of Stanford's suggestions including not assigning license plate until later (which means files need another name before validation), and changing what internally used files are plated and what are not. Now submission files are not plated, but files used in QA pipeline are
• src/hg/encode3/encodeDataWarehouse/edwAddQaEnrichTarget/makefile
  • lines changed 4, context: html, text, full: html, text
    Program to load a new enrichment target bed to database.
• src/hg/encode3/encodeDataWarehouse/edwAddSubscriber/makefile
  • lines changed 4, context: html, text, full: html, text
    Program to add subscriber - a program called when files are added.
• src/hg/encode3/encodeDataWarehouse/edwAddSubscriber/test.ra
  • lines changed 2, context: html, text, full: html, text
    Program to add subscriber - a program called when files are added.
• src/hg/encode3/encodeDataWarehouse/edwMakeEnrichments/edwMakeEnrichments.c
  • lines changed 144, context: html, text, full: html, text
    Starting to work on next pass - the part that calculates enrichments. Possibly have it running bwa twice in pipe to produce a sam file.
  • lines changed 158, context: html, text, full: html, text
    Look like have it calculating enrichments for bam and fastq files, but still need to save them in database.
  • lines changed 89, context: html, text, full: html, text
    Seems to work for fastq and bam.
  • lines changed 200, context: html, text, full: html, text
    Making enrichments work for bigBed files.
  • lines changed 118, context: html, text, full: html, text
    Making it so mouse and human have separate enrichment targets. Adding bigWig enrichment support.
  • lines changed 4, context: html, text, full: html, text
    Bringing structure commenting up to standards.
  • lines changed 32, context: html, text, full: html, text
    Implementing a number of Stanford's suggestions including not assigning license plate until later (which means files need another name before validation), and changing what internally used files are plated and what are not. Now submission files are not plated, but files used in QA pipeline are
  • lines changed 23, context: html, text, full: html, text
    Handling gtf and gff file enrichments.
• src/hg/encode3/encodeDataWarehouse/edwMakeEnrichments/makefile
  • lines changed 4, context: html, text, full: html, text
    Starting to work on next pass - the part that calculates enrichments. Possibly have it running bwa twice in pipe to produce a sam file.
• src/hg/encode3/encodeDataWarehouse/edwMakeReplicateQa/edwMakeReplicateQa.c
  • lines changed 105, context: html, text, full: html, text
    Starting to do replicate QA.
• src/hg/encode3/encodeDataWarehouse/edwMakeReplicateQa/makefile
  • lines changed 4, context: html, text, full: html, text
    Starting to do replicate QA.
• src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c
  • lines changed 162, context: html, text, full: html, text
    Getting started on first pass of after-upload validation.
  • lines changed 197, context: html, text, full: html, text
    Making makeValidFile count up items and create subsample files for fastq's and bams.
  • lines changed 95, context: html, text, full: html, text
    Switched to just system() calls with temp files from Mark's pipeline after some difficulty getting pipeline to behave robustly. Seems to work now.
  • lines changed 93, context: html, text, full: html, text
    Making scan through sam file keep a little more information.
  • lines changed 8, context: html, text, full: html, text
    Computing sample coverage.
  • lines changed 2, context: html, text, full: html, text
    Adding very light clipping to sampleBed so there are no negative chromStarts.
  • lines changed 130, context: html, text, full: html, text
    Implementing a number of Stanford's suggestions including not assigning license plate until later (which means files need another name before validation), and changing what internally used files are plated and what are not. Now submission files are not plated, but files used in QA pipeline are
  • lines changed 66, context: html, text, full: html, text
    Making it avoid validating something already validated.
• src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/makefile
  • lines changed 4, context: html, text, full: html, text
    Getting started on first pass of after-upload validation.
• src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c
  • lines changed 154, context: html, text, full: html, text
    Moving some code from edwSubmit to lib so as to share. Adding edwGetLocalFile routine.
  • lines changed 20, context: html, text, full: html, text
    Polishing bits of schema to do with encodeQa, and refactoring for qa pipeline.
  • lines changed 8, context: html, text, full: html, text
    Adding suffix or two back to edwFileName so auto uncompression works.
  • lines changed 18, context: html, text, full: html, text
    Implementing a number of Stanford's suggestions including not assigning license plate until later (which means files need another name before validation), and changing what internally used files are plated and what are not. Now submission files are not plated, but files used in QA pipeline are
  • lines changed 8, context: html, text, full: html, text
    Improving commenting.
  • lines changed 8, context: html, text, full: html, text
    Making edwSubmit not start fetching a file it is already fetching in another thread so often
• src/hg/encode3/encodeDataWarehouse/inc/edwLib.h
  • lines changed 33, context: html, text, full: html, text
    Moving some code from edwSubmit to lib so as to share. Adding edwGetLocalFile routine.
  • lines changed 4, context: html, text, full: html, text
    Adding suffix or two back to edwFileName so auto uncompression works.
  • lines changed 1, context: html, text, full: html, text
    Adding edwValDataDir global.
  • lines changed 21, context: html, text, full: html, text
    Implementing a number of Stanford's suggestions including not assigning license plate until later (which means files need another name before validation), and changing what internally used files are plated and what are not. Now submission files are not plated, but files used in QA pipeline are
  • lines changed 17, context: html, text, full: html, text
    Adding some functions for fetching edwFile and edwValidFile from database.
• src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h
  • lines changed 224, context: html, text, full: html, text
    Adding a bunch of new tables for automatic QA efforts.
  • lines changed 468, context: html, text, full: html, text
    Polishing bits of schema to do with encodeQa, and refactoring for qa pipeline.
  • lines changed 2, context: html, text, full: html, text
    Adding mapRatio field to validFile
  • lines changed 4, context: html, text, full: html, text
    Renaming samplePath to sampleBed since that's what it always is now. Adding flag 'gotMapRatio' so you can tell when that field is valid.
  • lines changed 2, context: html, text, full: html, text
    Removing gotMapRatio field, now we always have it.
  • lines changed 3, context: html, text, full: html, text
    Removing licensePlate from edwFile - it doesn't happen until validation.
• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
  • lines changed 277, context: html, text, full: html, text
    Moving some code from edwSubmit to lib so as to share. Adding edwGetLocalFile routine.
  • lines changed 45, context: html, text, full: html, text
    Adding suffix or two back to edwFileName so auto uncompression works.
  • lines changed 1, context: html, text, full: html, text
    Adding edwValDataDir global.
  • lines changed 139, context: html, text, full: html, text
    Implementing a number of Stanford's suggestions including not assigning license plate until later (which means files need another name before validation), and changing what internally used files are plated and what are not. Now submission files are not plated, but files used in QA pipeline are
  • lines changed 68, context: html, text, full: html, text
    Adding some functions for fetching edwFile and edwValidFile from database.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as
  • lines changed 48, context: html, text, full: html, text
    Adding a bunch of new tables for automatic QA efforts.
  • lines changed 43, context: html, text, full: html, text
    Polishing bits of schema to do with encodeQa, and refactoring for qa pipeline.
  • lines changed 1, context: html, text, full: html, text
    Adding mapRatio field to validFile
  • lines changed 3, context: html, text, full: html, text
    Renaming samplePath to sampleBed since that's what it always is now. Adding flag 'gotMapRatio' so you can tell when that field is valid.
  • lines changed 1, context: html, text, full: html, text
    Removing gotMapRatio field, now we always have it.
  • lines changed 2, context: html, text, full: html, text
    Removing licensePlate from edwFile - it doesn't happen until validation.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c
  • lines changed 528, context: html, text, full: html, text
    Adding a bunch of new tables for automatic QA efforts.
  • lines changed 1168, context: html, text, full: html, text
    Polishing bits of schema to do with encodeQa, and refactoring for qa pipeline.
  • lines changed 15, context: html, text, full: html, text
    Adding mapRatio field to validFile
  • lines changed 37, context: html, text, full: html, text
    Renaming samplePath to sampleBed since that's what it always is now. Adding flag 'gotMapRatio' so you can tell when that field is valid.
  • lines changed 17, context: html, text, full: html, text
    Removing gotMapRatio field, now we always have it.
  • lines changed 42, context: html, text, full: html, text
    Removing licensePlate from edwFile - it doesn't happen until validation.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql
  • lines changed 52, context: html, text, full: html, text
    Adding a bunch of new tables for automatic QA efforts.
  • lines changed 44, context: html, text, full: html, text
    Polishing bits of schema to do with encodeQa, and refactoring for qa pipeline.
  • lines changed 1, context: html, text, full: html, text
    Adding mapRatio field to validFile
  • lines changed 3, context: html, text, full: html, text
    Renaming samplePath to sampleBed since that's what it always is now. Adding flag 'gotMapRatio' so you can tell when that field is valid.
  • lines changed 1, context: html, text, full: html, text
    Removing gotMapRatio field, now we always have it.
  • lines changed 2, context: html, text, full: html, text
    Removing licensePlate from edwFile - it doesn't happen until validation.
• src/hg/encode3/encodeDataWarehouse/lib/redoSchema
  • lines changed 6, context: html, text, full: html, text
    Adding a bunch of new tables for automatic QA efforts.
  • lines changed 2, context: html, text, full: html, text
    Polishing bits of schema to do with encodeQa, and refactoring for qa pipeline.
• src/hg/encode3/encodeDataWarehouse/lib/resetEdw
  • lines changed 2, context: html, text, full: html, text
    Making reset script start up database with hg19 and mm9
  • lines changed 6, context: html, text, full: html, text
    Polishing bits of schema to do with encodeQa, and refactoring for qa pipeline.
  • lines changed 4, context: html, text, full: html, text
    Adding a few views to db init script.
  • lines changed 5, context: html, text, full: html, text
    Adding files view and mouse targets for enrichment analysis.
  • lines changed 10, context: html, text, full: html, text
    Implementing a number of Stanford's suggestions including not assigning license plate until later (which means files need another name before validation), and changing what internally used files are plated and what are not. Now submission files are not plated, but files used in QA pipeline are
• src/hg/encode3/encodeDataWarehouse/makefile
  • lines changed 5, context: html, text, full: html, text
    Putting in a bunch of new edw-related programs.
  • lines changed 2, context: html, text, full: html, text
    Starting to do replicate QA.
• src/hg/encode3/importEncode2/README
  • lines changed 4, context: html, text, full: html, text
    Improving docs a hair.
• src/hg/encode3/importEncode2/encode2MakeEncode3/encode2MakeEncode3.c
  • lines changed 2, context: html, text, full: html, text
    Making so a few more bigBeds get labeled as such in manifest - the ones made from GTF and BEDs in particular.
• src/hg/encode3/importEncode2/encode2Manifest/encode2Manifest.c
  • lines changed 4, context: html, text, full: html, text
    Changing 'regulatory' enrichment to 'open.'
• src/hg/encode3/importEncode2/encode2Meta/encode2Meta.c
  • lines changed 20, context: html, text, full: html, text
    adding database parameter to command line.
• src/hg/encode3/validateManifest/makefile
  • lines changed 2, context: html, text, full: html, text
    fixing allowed genomes (hg38 instead of hg36 oops), changing vm version comment to 2nd line since that makes it work with jims validated.txt loader code, added flush to tmp output
• src/hg/encode3/validateManifest/validateManifest.c
  • lines changed 7, context: html, text, full: html, text
    fixing allowed genomes (hg38 instead of hg36 oops), changing vm version comment to 2nd line since that makes it work with jims validated.txt loader code, added flush to tmp output
  • lines changed 31, context: html, text, full: html, text
    fixing some variable names to be conventional
  • lines changed 13, context: html, text, full: html, text
    adding simple gtf checking by running gffRead on the file; minor improvements in comments
  • lines changed 17, context: html, text, full: html, text
    improving bam handling
  • lines changed 25, context: html, text, full: html, text
    increment vm version to 1.2, added fileExists check early, make version comment clearer
  • lines changed 3, context: html, text, full: html, text
    adding support for format "unknown" as requested by jim
  • lines changed 13, context: html, text, full: html, text
    adding support for detecting validateFiles in the current directory and then using ./validateFiles in the commandline
  • lines changed 23, context: html, text, full: html, text
    added output_type, experiment, replicate, enriched_in as required fields
• src/hg/genePredToGtf/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    eliminate BINDIR from tests makefile, refs #9104
• src/hg/hgTables/mainPage.c
  • lines changed 1, context: html, text, full: html, text
    made link go directly to explanation of public MySQL server instead of to FAQ that says we have one, which requires an extra click to get there
• src/hg/hgTracks/retroGene.c
  • lines changed 2, context: html, text, full: html, text
    Added track handler for V5 of the Retroposed Genes track (ucscRetro).
• src/hg/hgc/hgdpClick.c
  • lines changed 8, context: html, text, full: html, text
    remove static mustRename() that was clashing to a global one defined in osunix.c
• src/hg/htdocs/ENCODE/FAQ/index.html
  • lines changed 1, context: html, text, full: html, text
    Added a second comma to a parenthetical phrase. refs #9712
  • lines changed 65, context: html, text, full: html, text
    Lowercasing TARGET, putting _blank in quotes, making links relative CR refs #9712 #10591
  • lines changed 0, context: html, text, full: html, text
    Adding space to HTML line, correctng format between href and target, CR ref# 10591
• src/hg/htdocs/ENCODE/index.html
  • lines changed 31, context: html, text, full: html, text
    Retire older news to archive, in preparation for adding info about new FAQ page. refs #9712
  • lines changed 69, context: html, text, full: html, text
    Add news and link for new FAQ page. Also add news item for January release of AWG Dnase tracks. refs #9712
• src/hg/htdocs/ENCODE/newsarch.html
  • lines changed 39, context: html, text, full: html, text
    Retire older news to archive, in preparation for adding info about new FAQ page. refs #9712
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 7, context: html, text, full: html, text
    added the command for mysql-public so you don't have to click again to get the minimum
• src/hg/htdocs/FAQ/FAQtracks.html
  • lines changed 1, context: html, text, full: html, text
    corrected last sentence. refs #4553
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 53, context: html, text, full: html, text
    added section on track hubs and sessions, refs #8519
  • lines changed 1, context: html, text, full: html, text
    added missing target=_blank attribute
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 19, context: html, text, full: html, text
    Removed url2 as a generic setting, since it is only supported by special case code. Also combined url/urlLabel into a single blurb and split out the hub specific version into a separate blurb. Finally, added a prompt to redirect hub contruibutors to the hub specific version of this document.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html
  • lines changed 12, context: html, text, full: html, text
    Removed url2 as a generic setting, since it is only supported by special case code. Also combined url/urlLabel into a single blurb and split out the hub specific version into a separate blurb. Finally, added a prompt to redirect hub contruibutors to the hub specific version of this document.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 40, context: html, text, full: html, text
    Removed url2 as a generic setting, since it is only supported by special case code. Also combined url/urlLabel into a single blurb and split out the hub specific version into a separate blurb. Finally, added a prompt to redirect hub contruibutors to the hub specific version of this document.
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 30, context: html, text, full: html, text
    Added link to Cancer Genomics Browser and an accompanying news item.
• src/hg/htdocs/index.html
  • lines changed 2, context: html, text, full: html, text
    Added link to Cancer Genomics Browser and an accompanying news item.
• src/hg/htdocs/indexNews.html
  • lines changed 80, context: html, text, full: html, text
    Added link to Cancer Genomics Browser and an accompanying news item.
  • lines changed 2, context: html, text, full: html, text
    Slight wording change in CB announcement.
• src/hg/inc/jksql.h
  • lines changed 3, context: html, text, full: html, text
    Added sqlQuickLongLong
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v282
• src/hg/lib/annoGratorGpVar.c
  • lines changed 64, context: html, text, full: html, text
    Use localmem for annoRow storage, instead of many independent malloc & free calls. refs #6152
• src/hg/lib/annoStreamDb.c
  • lines changed 40, context: html, text, full: html, text
    Use localmem for annoRow storage, instead of many independent malloc & free calls. refs #6152
  • lines changed 31, context: html, text, full: html, text
    Adding annoStreamTab and simple test case.refs #6152
    Performance will not be good for a series of queries to small regions
    on the same chromosome, because even if the regions don't overlap, we
    will have to reopen the file every time and start over just in case
    there are some items that start to the left of the region but overlap
    it.
    To fix that, we could add a queue for use when the region is smaller
    than a chromosome. Items that end to the right of the region would be
    kept in a queue in case they're needed in the next region query. When
    a new sub-chrom region query begins, if there are items in the queue
    that overlap the new region, they are used first and then we start
    reading from the file where we left off at the end of the last region.
    
• src/hg/lib/annoStreamWig.c
  • lines changed 5, context: html, text, full: html, text
    Use localmem for annoRow storage, instead of many independent malloc & free calls. refs #6152
• src/hg/lib/customFactory.c
  • lines changed 2, context: html, text, full: html, text
    limit custom track submissions to 1,000 tracks, and add references to Track Hub and Big Wig help when limits prevent custom tracks refs #10599
• src/hg/lib/jksql.c
  • lines changed 15, context: html, text, full: html, text
    Added sqlQuickLongLong
• src/hg/lib/tests/annoGratorTester.c
  • lines changed 24, context: html, text, full: html, text
    Adding annoStreamTab and simple test case.refs #6152
    Performance will not be good for a series of queries to small regions
    on the same chromosome, because even if the regions don't overlap, we
    will have to reopen the file every time and start over just in case
    there are some items that start to the left of the region but overlap
    it.
    To fix that, we could add a queue for use when the region is smaller
    than a chromosome. Items that end to the right of the region would be
    kept in a queue in case they're needed in the next region query. When
    a new sub-chrom region query begins, if there are items in the queue
    that overlap the new region, they are used first and then we start
    reading from the file where we left off at the end of the last region.
    
• src/hg/lib/tests/annoGratorTests.mk
  • lines changed 1, context: html, text, full: html, text
    Adding annoStreamTab and simple test case.refs #6152
    Performance will not be good for a series of queries to small regions
    on the same chromosome, because even if the regions don't overlap, we
    will have to reopen the file every time and start over just in case
    there are some items that start to the left of the region but overlap
    it.
    To fix that, we could add a queue for use when the region is smaller
    than a chromosome. Items that end to the right of the region would be
    kept in a queue in case they're needed in the next region query. When
    a new sub-chrom region query begins, if there are items in the queue
    that overlap the new region, they are used first and then we start
    reading from the file where we left off at the end of the last region.
    
• src/hg/lib/ucscRetroInfo.c
  • lines changed 2, context: html, text, full: html, text
    Changed size of row array to match the new ucscRetroInfo table size after a column was dropped.
• src/hg/lib/wigAsciiToBinary.c
  • lines changed 2, context: html, text, full: html, text
    limit custom track submissions to 1,000 tracks, and add references to Track Hub and Big Wig help when limits prevent custom tracks refs #10599
• src/hg/liftOver/tests/makefile
  • lines changed 17, context: html, text, full: html, text
    eliminate BINDIR from tests makefile, refs #9104
• src/hg/makeDb/doc/encodeAwgHg19.txt
  • lines changed 12, context: html, text, full: html, text
    Add two more scoring methods (2 std devs, asinh). refs #10569
  • lines changed 188, context: html, text, full: html, text
    Add quality term to CV. Create release notes. refs #10042
  • lines changed 1, context: html, text, full: html, text
    Wrap-up for QA. refs #10042
  • lines changed 1, context: html, text, full: html, text
    Wrap-up for QA. refs #10042
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeAwgTfbsUniform.release1.notes
  • lines changed 40, context: html, text, full: html, text
    Add quality term to CV. Create release notes. refs #10042
  • lines changed 3, context: html, text, full: html, text
    Update release notes. refs #10042
• src/hg/makeDb/hgLoadMaf/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    eliminate BINDIR from tests makefile, refs #9104
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 30, context: html, text, full: html, text
    Add quality term to CV. Create release notes. refs #10042
  • lines changed 2, context: html, text, full: html, text
    Correcting description of SPP peaks to match optimal and conserved to term
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 32, context: html, text, full: html, text
    Copying alpha/cv.ra to beta/cv.ra, adjusting desc SPP peaks, adding quality for TFBS uniform release refs #10042
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAwgTfbsUniform.ra
  • lines changed 691, context: html, text, full: html, text
    Update md5sums after adding scores to download files. refs #10042
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgTfbsUniform.html
  • lines changed 5, context: html, text, full: html, text
    Update track description (quality, filtering). refs #10042
  • lines changed 1, context: html, text, full: html, text
    Fix a URL. refs #10042
  • lines changed 9, context: html, text, full: html, text
    Add info about score to track description. refs #10042
  • lines changed 124, context: html, text, full: html, text
    Reformat to <=100 lines. refs #10042
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    implementing minimal makefile userApp.mk refs #9104
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    implementing minimal makefile userApp.mk refs #9104
• src/hg/oneShot/freen/freen.c
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    Learning pipeline api again.
• src/hg/phyloGif/makefile
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    correctly use DESTDIR with BINDIR refs #9104
• src/hg/pslCDnaFilter/tests/makefile
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    eliminate BINDIR from tests makefile, refs #9104
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    do not use BINDIR in the tests makefile to reference the test program
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    eliminate BINDIR from tests makefile, refs #9104
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    implementing minimal makefile userApp.mk refs #9104
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    perhaps last lot of makefiles converted to new minimal style refs #9104
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    perhaps last lot of makefiles converted to new minimal style refs #9104
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    perhaps last lot of makefiles converted to new minimal style refs #9104
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    small change to otto GWAS makefile
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    ignore another non-Unicode character
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    do not use BINDIR in the tests makefile to reference the test program
• src/hg/utils/positionalTblCheck/makefile
  • lines changed 14, context: html, text, full: html, text
    perhaps last lot of makefiles converted to new minimal style refs #9104
• src/hg/utils/pslMap/tests/makefile
  • lines changed 2, context: html, text, full: html, text
    do not use BINDIR in the tests makefile to reference the test program
• src/hg/utils/pslUniq/makefile
  • lines changed 17, context: html, text, full: html, text
    perhaps last lot of makefiles converted to new minimal style refs #9104
• src/hg/utils/refSeqGet/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    do not use BINDIR in the tests makefile to reference the test program
• src/hg/utils/refreshNamedSessionCustomTracks/makefile
  • lines changed 19, context: html, text, full: html, text
    perhaps last lot of makefiles converted to new minimal style refs #9104
• src/hg/utils/safePush/makefile
  • lines changed 14, context: html, text, full: html, text
    perhaps last lot of makefiles converted to new minimal style refs #9104
• src/hg/utils/toDev64/makefile
  • lines changed 14, context: html, text, full: html, text
    perhaps last lot of makefiles converted to new minimal style refs #9104
• src/hg/utils/twoBitMask/makefile
  • lines changed 16, context: html, text, full: html, text
    perhaps last lot of makefiles converted to new minimal style refs #9104
• src/hg/utils/wigBedToStep/makefile
  • lines changed 14, context: html, text, full: html, text
    perhaps last lot of makefiles converted to new minimal style refs #9104
• src/inc/annoGrator.h
  • lines changed 4, context: html, text, full: html, text
    Use localmem for annoRow storage, instead of many independent malloc & free calls. refs #6152
• src/inc/annoRow.h
  • lines changed 15, context: html, text, full: html, text
    Use localmem for annoRow storage, instead of many independent malloc & free calls. refs #6152
• src/inc/annoStreamTab.h
  • lines changed 12, context: html, text, full: html, text
    Adding annoStreamTab and simple test case.refs #6152
    Performance will not be good for a series of queries to small regions
    on the same chromosome, because even if the regions don't overlap, we
    will have to reopen the file every time and start over just in case
    there are some items that start to the left of the region but overlap
    it.
    To fix that, we could add a queue for use when the region is smaller
    than a chromosome. Items that end to the right of the region would be
    kept in a queue in case they're needed in the next region query. When
    a new sub-chrom region query begins, if there are items in the queue
    that overlap the new region, they are used first and then we start
    reading from the file where we left off at the end of the last region.
    
• src/inc/annoStreamer.h
  • lines changed 1, context: html, text, full: html, text
    Use localmem for annoRow storage, instead of many independent malloc & free calls. refs #6152
  • lines changed 8, context: html, text, full: html, text
    Adding annoStreamTab and simple test case.refs #6152
    Performance will not be good for a series of queries to small regions
    on the same chromosome, because even if the regions don't overlap, we
    will have to reopen the file every time and start over just in case
    there are some items that start to the left of the region but overlap
    it.
    To fix that, we could add a queue for use when the region is smaller
    than a chromosome. Items that end to the right of the region would be
    kept in a queue in case they're needed in the next region query. When
    a new sub-chrom region query begins, if there are items in the queue
    that overlap the new region, they are used first and then we start
    reading from the file where we left off at the end of the last region.
    
• src/inc/bamFile.h
  • lines changed 6, context: html, text, full: html, text
    Adding samToBed and samToOpenBed functions.
• src/inc/basicBed.h
  • lines changed 12, context: html, text, full: html, text
    Adding some more bed3 routines - for the minimalists.
• src/inc/cheapcgi.h
  • lines changed 15, context: html, text, full: html, text
    Adding cgiParsedVars - something that makes it easier to use the cgi var parser.
• src/inc/portable.h
  • lines changed 3, context: html, text, full: html, text
    Adding makeSymLink
  • lines changed 3, context: html, text, full: html, text
    Adding mustRename wrapper around rename().
• src/isPcr/gfPcr/makefile
  • lines changed 2, context: html, text, full: html, text
    correctly using DESTDIR with BINDIR refs #9104
• src/isPcr/isPcr/makefile
  • lines changed 2, context: html, text, full: html, text
    correctly using DESTDIR with BINDIR refs #9104
• src/lib/annoGrateWig.c
  • lines changed 34, context: html, text, full: html, text
    Use localmem for annoRow storage, instead of many independent malloc & free calls. refs #6152
• src/lib/annoGrator.c
  • lines changed 26, context: html, text, full: html, text
    Use localmem for annoRow storage, instead of many independent malloc & free calls. refs #6152
• src/lib/annoGratorQuery.c
  • lines changed 9, context: html, text, full: html, text
    Use localmem for annoRow storage, instead of many independent malloc & free calls. refs #6152
• src/lib/annoRow.c
  • lines changed 72, context: html, text, full: html, text
    Use localmem for annoRow storage, instead of many independent malloc & free calls. refs #6152
• src/lib/annoStreamBigBed.c
  • lines changed 3, context: html, text, full: html, text
    Use localmem for annoRow storage, instead of many independent malloc & free calls. refs #6152
• src/lib/annoStreamBigWig.c
  • lines changed 5, context: html, text, full: html, text
    Use localmem for annoRow storage, instead of many independent malloc & free calls. refs #6152
• src/lib/annoStreamTab.c
  • lines changed 214, context: html, text, full: html, text
    Adding annoStreamTab and simple test case.refs #6152
    Performance will not be good for a series of queries to small regions
    on the same chromosome, because even if the regions don't overlap, we
    will have to reopen the file every time and start over just in case
    there are some items that start to the left of the region but overlap
    it.
    To fix that, we could add a queue for use when the region is smaller
    than a chromosome. Items that end to the right of the region would be
    kept in a queue in case they're needed in the next region query. When
    a new sub-chrom region query begins, if there are items in the queue
    that overlap the new region, they are used first and then we start
    reading from the file where we left off at the end of the last region.
    
• src/lib/annoStreamVcf.c
  • lines changed 2, context: html, text, full: html, text
    Use localmem for annoRow storage, instead of many independent malloc & free calls. refs #6152
• src/lib/annoStreamer.c
  • lines changed 43, context: html, text, full: html, text
    Adding annoStreamTab and simple test case.refs #6152
    Performance will not be good for a series of queries to small regions
    on the same chromosome, because even if the regions don't overlap, we
    will have to reopen the file every time and start over just in case
    there are some items that start to the left of the region but overlap
    it.
    To fix that, we could add a queue for use when the region is smaller
    than a chromosome. Items that end to the right of the region would be
    kept in a queue in case they're needed in the next region query. When
    a new sub-chrom region query begins, if there are items in the queue
    that overlap the new region, they are used first and then we start
    reading from the file where we left off at the end of the last region.
    
• src/lib/bamFile.c
  • lines changed 54, context: html, text, full: html, text
    Adding samToBed and samToOpenBed functions.
  • lines changed 2, context: html, text, full: html, text
    Fixing strict-gcc warning "‘return’ with a value, in function returning void"
• src/lib/basicBed.c
  • lines changed 1, context: html, text, full: html, text
    Fixed bug where bed loader was segfaulting on beds with less than 9 fields.
  • lines changed 53, context: html, text, full: html, text
    Adding some more bed3 routines - for the minimalists.
• src/lib/cheapcgi.c
  • lines changed 34, context: html, text, full: html, text
    Adding cgiParsedVars - something that makes it easier to use the cgi var parser.
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding annoStreamTab and simple test case.refs #6152
    Performance will not be good for a series of queries to small regions
    on the same chromosome, because even if the regions don't overlap, we
    will have to reopen the file every time and start over just in case
    there are some items that start to the left of the region but overlap
    it.
    To fix that, we could add a queue for use when the region is smaller
    than a chromosome. Items that end to the right of the region would be
    kept in a queue in case they're needed in the next region query. When
    a new sub-chrom region query begins, if there are items in the queue
    that overlap the new region, they are used first and then we start
    reading from the file where we left off at the end of the last region.
    
• src/lib/osunix.c
  • lines changed 8, context: html, text, full: html, text
    Adding makeSymLink
  • lines changed 3, context: html, text, full: html, text
    Made rTempName tolerate a trailing slash in dir name.
  • lines changed 8, context: html, text, full: html, text
    Adding mustRename wrapper around rename().
• src/utils/bedScore/bedScore.c
  • lines changed 103, context: html, text, full: html, text
    Add two more scoring methods (2 std devs, asinh). refs #10569
• src/utils/bedScore/tests/expected/broadGm12878Ctcf.jan2011.asinh.narrowPeak
  • lines changed 40006, context: html, text, full: html, text
    Add tests for std2 and asinh scoring methods. refs #10569
• src/utils/bedScore/tests/expected/encodeStd2Test.bed
  • lines changed 44159, context: html, text, full: html, text
    Fix test makefile to work with default targets from build dir. refs #10569
• src/utils/bedScore/tests/expected/uniform.bed
  • lines changed 20, context: html, text, full: html, text
    Add tests for std2 and asinh scoring methods. refs #10569
• src/utils/bedScore/tests/input/broadGm12878Ctcf.jan2011.asinh.narrowPeak
  • lines changed 40006, context: html, text, full: html, text
    Add tests for std2 and asinh scoring methods. refs #10569
• src/utils/bedScore/tests/input/uniform.bed
  • lines changed 20, context: html, text, full: html, text
    Add tests for std2 and asinh scoring methods. refs #10569
• src/utils/bedScore/tests/makefile
  • lines changed 13, context: html, text, full: html, text
    Add tests for std2 and asinh scoring methods. refs #10569
  • lines changed 21, context: html, text, full: html, text
    Fix test makefile to work with default targets from build dir. refs #10569
  • lines changed 3, context: html, text, full: html, text
    More clean-up of makefile to fit well in new makefile scheme
  • lines changed 1, context: html, text, full: html, text
    do not use BINDIR in the tests makefile to reference the test program
• src/utils/bedToBigBed/bedToBigBed.c
  • lines changed 2, context: html, text, full: html, text
    Sorting before building index.
• src/utils/bigBedInfo/bigBedInfo.c
  • lines changed 6, context: html, text, full: html, text
    Made bigBedInfo -extraIndex give you item count and field offset too.
• src/utils/convolve/tests/makefile
  • lines changed 5, context: html, text, full: html, text
    add makefile for running tests refs #9104
• src/utils/htmlCheck/htmlCheck.c
  • lines changed 1, context: html, text, full: html, text
    changed usage to mention that question marks do not resolve unless url is in quotes
• src/utils/pslLiftSubrangeBlat/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    eliminate BINDIR from tests makefile, refs #9104
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v282 final build
• src/utils/twoBitDup/twoBitDup.c
  • lines changed 4, context: html, text, full: html, text
    add udcDir option to the twoBit utilities so they can access remote twoBits with something other than the default udc cache dir
• src/utils/twoBitInfo/twoBitInfo.c
  • lines changed 4, context: html, text, full: html, text
    add udcDir option to the twoBit utilities so they can access remote twoBits with something other than the default udc cache dir
• src/utils/twoBitToFa/twoBitToFa.c
  • lines changed 4, context: html, text, full: html, text
    add udcDir option to the twoBit utilities so they can access remote twoBits with something other than the default udc cache dir

• lines changed: 134914
• files changed: 356