File Changes for kent

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

• 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/inc/jksql.h
  • lines changed 3, context: html, text, full: html, text
    Added sqlQuickLongLong
• src/hg/lib/jksql.c
  • lines changed 15, context: html, text, full: html, text
    Added sqlQuickLongLong
• src/hg/oneShot/freen/freen.c
  • lines changed 21, context: html, text, full: html, text
    Learning pipeline api again.
• 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/lib/bamFile.c
  • lines changed 54, context: html, text, full: html, text
    Adding samToBed and samToOpenBed functions.
• 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/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/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.