File Changes for cricket

v266_preview to v266_preview2 (2012-04-10 to 2012-04-17) v266

• src/hg/encode/autoSql/README
  • lines changed 3, context: html, text, full: html, text
    Moving the as files to the lib/encode directory so they are all together at least.
• src/hg/encode/autoSql/bedLogR.as
  • lines changed 14, context: html, text, full: html, text
    Moving the as files to the lib/encode directory so they are all together at least.
• src/hg/encode/autoSql/bedLogR.sql
  • lines changed 22, context: html, text, full: html, text
    Moving the as files to the lib/encode directory so they are all together at least.
• src/hg/encode/autoSql/bedRnaElements.as
  • lines changed 13, context: html, text, full: html, text
    Moving the as files to the lib/encode directory so they are all together at least.
• src/hg/encode/autoSql/bedRnaElements.sql
  • lines changed 20, context: html, text, full: html, text
    Moving the as files to the lib/encode directory so they are all together at least.
• src/hg/encode/autoSql/bedRrbs.as
  • lines changed 15, context: html, text, full: html, text
    Moving the as files to the lib/encode directory so they are all together at least.
• src/hg/encode/autoSql/bedRrbs.sql
  • lines changed 23, context: html, text, full: html, text
    Moving the as files to the lib/encode directory so they are all together at least.
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 202, context: html, text, full: html, text
    DEPRECATING OLD FORMATS1) Changed the order of formatChecker to group like with like 2) Changed wig and bedGraph validation to say submit as a bigWig 3) Changed fasta to say submit as a fastQ 4) Dropped peptideMapping and rpkm as one was a freepass and the other was an ill defined special case format for Caltech 5) Dropped PSL as we don't accept it, but kept code so that we could have it on file. 6) Changed tagAlign and pairedTagAligh to say submit as BAM 7) I also kept the bedGraph validator as example code in the comments, not sure if we need it 8) I left bedFloat and csqual and csfasta as I do not have clear directive.
• src/hg/encode/geoSofts/ucsc_encode_dcc_wgEncodeCaltechRnaSeq.hg18.soft
  • lines changed 1712, context: html, text, full: html, text
    moved to downloads dir, these shouldnt be in the tree
• src/hg/encode/geoSofts/ucsc_encode_dcc_wgEncodeCshlLongRnaSeq.hg18.soft
  • lines changed 111, context: html, text, full: html, text
    moved to downloads dir, these shouldnt be in the tree
• src/hg/encode/geoSofts/ucsc_encode_dcc_wgEncodeCshlShortRnaSeq.hg18.soft
  • lines changed 339, context: html, text, full: html, text
    moved to downloads dir, these shouldnt be in the tree
• src/hg/encode/geoSofts/ucsc_encode_dcc_wgEncodeCshlShortRnaSeq.hg19.soft
  • lines changed 407, context: html, text, full: html, text
    moved to downloads dir, these shouldnt be in the tree
• src/hg/encode/geoSofts/ucsc_encode_dcc_wgEncodeUwChIPSeq.hg18.soft
  • lines changed 4436, context: html, text, full: html, text
    moved to downloads dir, these shouldnt be in the tree
• src/hg/encode/geoSofts/ucsc_encode_dcc_wgEncodeUwDgf.hg19.soft
  • lines changed 448, context: html, text, full: html, text
    moved to downloads dir, these shouldnt be in the tree
• src/hg/encode/validateFiles/tests/goodFemaleHg18.gappedPeak
  • lines changed 13, context: html, text, full: html, text
    Adding and improving test cases
• src/hg/encode/validateFiles/tests/goodFemaleHg19.bed10
  • lines changed 34, context: html, text, full: html, text
    Adding and improving test cases
• src/hg/encode/validateFiles/tests/goodFemaleHg19.bed11
  • lines changed 35, context: html, text, full: html, text
    Adding and improving test cases
• src/hg/encode/validateFiles/tests/goodFemaleHg19.bed12
  • lines changed 35, context: html, text, full: html, text
    Adding and improving test cases
• src/hg/encode/validateFiles/tests/goodFemaleHg19.narrowPeak
  • lines changed 40, context: html, text, full: html, text
    Adding more test files
• src/hg/encode/validateFiles/tests/goodHg18.fasta
  • lines changed 50, context: html, text, full: html, text
    Adding and improving test cases
• src/hg/encode/validateFiles/tests/goodHg19.csfasta
  • lines changed 49, context: html, text, full: html, text
    Adding and improving test cases
• src/hg/encode/validateFiles/tests/goodHg19.csqual
  • lines changed 49, context: html, text, full: html, text
    Adding and improving test cases
• src/hg/encode/validateFiles/tests/goodHg19.fastq
  • lines changed 100, context: html, text, full: html, text
    Adding more test files
• src/hg/encode/validateFiles/tests/goodMaleHg18.bedGraph
  • lines changed 29, context: html, text, full: html, text
    Adding more test files
• src/hg/encode/validateFiles/tests/goodMaleHg18.pairedTagAlign
  • lines changed 63, context: html, text, full: html, text
    Start of a test suite
• src/hg/encode/validateFiles/tests/goodMaleHg18.tagAlign
  • lines changed 150, context: html, text, full: html, text
    Start of a test suite
• src/hg/encode/validateFiles/tests/goodMaleHg19.bed3
  • lines changed 90, context: html, text, full: html, text
    Start of a test suite
• src/hg/encode/validateFiles/tests/goodMaleHg19.bed4
  • lines changed 92, context: html, text, full: html, text
    Start of a test suite
• src/hg/encode/validateFiles/tests/goodMaleHg19.bed5
  • lines changed 91, context: html, text, full: html, text
    Start of a test suite
• src/hg/encode/validateFiles/tests/goodMaleHg19.bed6
  • lines changed 91, context: html, text, full: html, text
    Start of a test suite
• src/hg/encode/validateFiles/tests/goodMaleHg19.bed7
  • lines changed 141884, context: html, text, full: html, text
    Adding more test files
• src/hg/encode/validateFiles/tests/goodMaleHg19.bed8
  • lines changed 141885, context: html, text, full: html, text
    Adding more test files
  • lines changed 3, context: html, text, full: html, text
    Adding and improving test cases
• src/hg/encode/validateFiles/tests/goodMaleHg19.bed9
  • lines changed 141886, context: html, text, full: html, text
    Adding more test files
  • lines changed 3, context: html, text, full: html, text
    Adding and improving test cases
• src/hg/encode/validateFiles/tests/goodMaleHg19.bedRrbs
  • lines changed 141887, context: html, text, full: html, text
    Adding more test files
  • lines changed 5, context: html, text, full: html, text
    Adding and improving test cases
• src/hg/encode/validateFiles/tests/goodMaleHg19.broadPeak
  • lines changed 94, context: html, text, full: html, text
    Start of a test suite
  • lines changed 1, context: html, text, full: html, text
    Removed an extra tab and the zero length line
• src/hg/encode/validateFiles/tests/goodMaleHg19.broadPeak.gz
  • lines changed 0, context: html, text, full: html, text
    Start of a test suite
• src/hg/encode/validateFiles/tests/goodMalehg19.bedRnaElements
  • lines changed 624500, context: html, text, full: html, text
    Start of a test suite
• src/hg/encode/validateFiles/tests/goodNoGenderHg19.bed15
  • lines changed 40, context: html, text, full: html, text
    Adding and improving test cases
• src/hg/encode/validateFiles/tests/goodNoGenderHg19.bedLogR
  • lines changed 69, context: html, text, full: html, text
    Adding more test files
• src/hg/encode/validateFiles/validateFilesUsage
  • lines changed 30, context: html, text, full: html, text
    Ever improving usage statement
• src/hg/lib/encode/bedLogR.as
  • lines changed 14, context: html, text, full: html, text
    Moving the as files to the lib/encode directory so they are all together at least.
  • lines changed 4, context: html, text, full: html, text
    First attempt at trying to clean up the as files to fit bed standard. Tried to make all strand char[1] and all reserved uint and have standard descriptions
• src/hg/lib/encode/bedLogR.sql
  • lines changed 22, context: html, text, full: html, text
    Moving the as files to the lib/encode directory so they are all together at least.
• src/hg/lib/encode/bedRnaElements.as
  • lines changed 13, context: html, text, full: html, text
    Moving the as files to the lib/encode directory so they are all together at least.
  • lines changed 5, context: html, text, full: html, text
    First attempt at trying to clean up the as files to fit bed standard. Tried to make all strand char[1] and all reserved uint and have standard descriptions
• src/hg/lib/encode/bedRnaElements.sql
  • lines changed 20, context: html, text, full: html, text
    Moving the as files to the lib/encode directory so they are all together at least.
• src/hg/lib/encode/bedRrbs.as
  • lines changed 15, context: html, text, full: html, text
    Moving the as files to the lib/encode directory so they are all together at least.
  • lines changed 4, context: html, text, full: html, text
    First attempt at trying to clean up the as files to fit bed standard. Tried to make all strand char[1] and all reserved uint and have standard descriptions
• src/hg/lib/encode/bedRrbs.sql
  • lines changed 23, context: html, text, full: html, text
    Moving the as files to the lib/encode directory so they are all together at least.
• src/hg/lib/encode/broadPeak.as
  • lines changed 5, context: html, text, full: html, text
    First attempt at trying to clean up the as files to fit bed standard. Tried to make all strand char[1] and all reserved uint and have standard descriptions
• src/hg/lib/encode/chiaPet.as
  • lines changed 1, context: html, text, full: html, text
    First attempt at trying to clean up the as files to fit bed standard. Tried to make all strand char[1] and all reserved uint and have standard descriptions
  • lines changed 12, context: html, text, full: html, text
    Chia pet was never used, we used bed12 instead. shortFrags are download only
• src/hg/lib/encode/chiaPet.sql
  • lines changed 19, context: html, text, full: html, text
    Chia pet was never used, we used bed12 instead. shortFrags are download only
• src/hg/lib/encode/cshlShortTransfrag.as
  • lines changed 30, context: html, text, full: html, text
    First attempt at trying to clean up the as files to fit bed standard. Tried to make all strand char[1] and all reserved uint and have standard descriptions
• src/hg/lib/encode/gappedPeak.as
  • lines changed 4, context: html, text, full: html, text
    First attempt at trying to clean up the as files to fit bed standard. Tried to make all strand char[1] and all reserved uint and have standard descriptions
  • lines changed 1, context: html, text, full: html, text
    Changing score to int to match bed standard
• src/hg/lib/encode/narrowPeak.as
  • lines changed 6, context: html, text, full: html, text
    First attempt at trying to clean up the as files to fit bed standard. Tried to make all strand char[1] and all reserved uint and have standard descriptions
• src/hg/lib/encode/obsolete/shortFrags.as
  • lines changed 31, context: html, text, full: html, text
    Chia pet was never used, we used bed12 instead. shortFrags are download only
• src/hg/lib/encode/obsolete/shortFrags.sql
  • lines changed 37, context: html, text, full: html, text
    Chia pet was never used, we used bed12 instead. shortFrags are download only
• src/hg/lib/encode/shortFrags.as
  • lines changed 31, context: html, text, full: html, text
    Chia pet was never used, we used bed12 instead. shortFrags are download only
• src/hg/lib/encode/shortFrags.sql
  • lines changed 37, context: html, text, full: html, text
    Chia pet was never used, we used bed12 instead. shortFrags are download only
• src/hg/lib/encode/tagAlign.as
  • lines changed 1, context: html, text, full: html, text
    First attempt at trying to clean up the as files to fit bed standard. Tried to make all strand char[1] and all reserved uint and have standard descriptions
• src/hg/lib/encode/wgEncodeGencodeExonSupport.as
  • lines changed 3, context: html, text, full: html, text
    Makeing the chromStart and chromEnd standard uint and standardizing the descriptions
  • lines changed 1, context: html, text, full: html, text
    First attempt at trying to clean up the as files to fit bed standard. Tried to make all strand char[1] and all reserved uint and have standard descriptions
• src/hg/lib/encode/wgEncodeGencodePolyAFeature.as
  • lines changed 7, context: html, text, full: html, text
    Makeing the chromStart and chromEnd standard uint and standardizing the descriptions
  • lines changed 2, context: html, text, full: html, text
    First attempt at trying to clean up the as files to fit bed standard. Tried to make all strand char[1] and all reserved uint and have standard descriptions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.ra
  • lines changed 22, context: html, text, full: html, text
    Fixing short labels to be shorter
  • lines changed 22, context: html, text, full: html, text
    Fixing steves requests #1664