File Changes for wong

v255_base to v256_preview (2011-08-08 to 2011-08-16) v256

• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • lines changed 1, context: html, text, full: html, text
    removed old comment from before we had design finalized
  • lines changed 1, context: html, text, full: html, text
    extra .txt extension in variable, removed from open statement
• src/hg/encode/encodeMkFilesList/encodeMkFilesList
  • lines changed 1, context: html, text, full: html, text
    fixed a message
  • lines changed 1, context: html, text, full: html, text
    an unless turned into an if, i got a little too exited with the unless statements, resulted in a logic error. Everytime a md5sum last modified date existed, it would get 0 as it's last modified date, i wanted that for files that didn't exist the last time md5sum was ran only. an unless is equivalent to if not (if !(condition));
  • lines changed 2, context: html, text, full: html, text
    changed verbosity level for some debugging prints\n
  • lines changed 88, context: html, text, full: html, text
    added functionality to put md5sum in metaDb
  • lines changed 14, context: html, text, full: html, text
    added in function to bot put bai in md5sum for bam if bai is missing
  • lines changed 1, context: html, text, full: html, text
    previous commit bot = not, this one i removed a variable i didn't use
  • lines changed 303, context: html, text, full: html, text
    lots of changes, more fleshed out comments, and found some bugs, namely the multiple regex match bug. added functionality to detect file bas name collisions, for table lookup purposes.
  • lines changed 25, context: html, text, full: html, text
    made functionality to check if there if an existing metaDb entry per file, if there is no corresponding fileName entry, it assumes orphaned, and warns you. In addition to that, I added functionality to make an inverted hash of md5sums and file names to check if there are collisions with regards to md5sums.
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhTfbs.release1.notes
  • lines changed 2020, context: html, text, full: html, text
    updated notes file for new files and name changes
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwDnase.release3.notes
  • lines changed 217, context: html, text, full: html, text
    updated notes file for uw dnase and uw histone
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwHistone.release2.notes
  • lines changed 255, context: html, text, full: html, text
    updated notes file for uw dnase and uw histone
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwTfbs.release2.notes
  • lines changed 448, context: html, text, full: html, text
    updated the release2 notes
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 36, context: html, text, full: html, text
    commented out k562b and hepg2b
  • lines changed 2, context: html, text, full: html, text
    changed t-rex-hek293 to hek293-t-rex
  • lines changed 2, context: html, text, full: html, text
    changed fetalpbde to pdbefetal
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 39, context: html, text, full: html, text
    fixed metadata issue
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwChIPSeq.ra
  • lines changed 21, context: html, text, full: html, text
    fixed metadata errors
• src/hg/makeDb/trackDb/human/hg18/wgEncodeSangerGencode.html
  • lines changed 2, context: html, text, full: html, text
    cleaned up gencode's references
  • lines changed 9, context: html, text, full: html, text
    alphabetized references
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
  • lines changed 1, context: html, text, full: html, text
    modified makefile
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAffyRnaChip.ra
  • lines changed 53, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 945, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHmm.ra
  • lines changed 10, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 163, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 1243, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 145, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeDukeAffyExon.ra
  • lines changed 106, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencode.ra
  • lines changed 55, context: html, text, full: html, text
    renamed wgEncodeGencode.ra to wgEncodeGencodeV3.ra
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV3.ra
  • lines changed 55, context: html, text, full: html, text
    renamed wgEncodeGencode.ra to wgEncodeGencodeV3.ra
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV4.ra
  • lines changed 17, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV7.ra
  • lines changed 16, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra
  • lines changed 69, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisDnaPet.ra
  • lines changed 35, context: html, text, full: html, text
    added md5sums
  • lines changed 7, context: html, text, full: html, text
    updated md5sums for colliding file names
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
  • lines changed 215, context: html, text, full: html, text
    added md5sums
  • lines changed 2, context: html, text, full: html, text
    corrected some md5 errors, there were colliding file names
  • lines changed 62, context: html, text, full: html, text
    updated md5sums for colliding file names
  • lines changed 3, context: html, text, full: html, text
    updated some md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaSeq.ra
  • lines changed 19, context: html, text, full: html, text
    added md5sums
  • lines changed 5, context: html, text, full: html, text
    updated md5sums for colliding file names
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibGenotype.ra
  • lines changed 89, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethyl450.ra
  • lines changed 12, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylArray.ra
  • lines changed 74, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
  • lines changed 405, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra
  • lines changed 101, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibRnaSeq.ra
  • lines changed 168, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 5, context: html, text, full: html, text
    revoked SL1196
  • lines changed 1696, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeMapability.ra
  • lines changed 11, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 285, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 347, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
  • lines changed 189, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromSynth.ra
  • lines changed 18, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 183, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyTiling.ra
  • lines changed 9, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyRipSeq.ra
  • lines changed 17, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunySwitchgear.ra
  • lines changed 3, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 109, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhNsome.ra
  • lines changed 63, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhRnaSeq.ra
  • lines changed 13, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 1839, context: html, text, full: html, text
    added md5sums
  • lines changed 129, context: html, text, full: html, text
    changed sc582 > sc584, and added in new objects
  • lines changed 257, context: html, text, full: html, text
    loaded last bits of sydh tfbs
  • lines changed 873, context: html, text, full: html, text
    changed t-rex-hek293 > hek293-t-rex and fetalpbde > pbdefetal
  • lines changed 19, context: html, text, full: html, text
    inserted md5sums for new files
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUchicagoTfbs.ra
  • lines changed 69, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUmassDekker5C.ra
  • lines changed 9, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra
  • lines changed 11, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUw5C.ra
  • lines changed 39, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra
  • lines changed 136, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 115, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 811, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 434, context: html, text, full: html, text
    loaded new uw tracks
  • lines changed 956, context: html, text, full: html, text
    added md5sums
  • lines changed 1, context: html, text, full: html, text
    added treatment as an expvar
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
  • lines changed 1405, context: html, text, full: html, text
    loaded new uw tracks
  • lines changed 73, context: html, text, full: html, text
    added one more submission 4696
  • lines changed 732, context: html, text, full: html, text
    added md5sums
  • lines changed 1, context: html, text, full: html, text
    added treatment as an expvar
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV3.html
  • lines changed 9, context: html, text, full: html, text
    cleaned up references for gencode hg19
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV3.ra
  • lines changed 3, context: html, text, full: html, text
    removed metadata lines
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.html
  • lines changed 2, context: html, text, full: html, text
    commented out multi view section
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
  • lines changed 16, context: html, text, full: html, text
    revoked SL1196
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhNsome.html
  • lines changed 1, context: html, text, full: html, text
    changed milli liters to microliters
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.html
  • lines changed 5, context: html, text, full: html, text
    sydh tfbs html fixes at QA's request
  • lines changed 1, context: html, text, full: html, text
    forgot snyder is part of stanford now
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
  • lines changed 25, context: html, text, full: html, text
    changed sc582 > sc584, and added in new objects
  • lines changed 177, context: html, text, full: html, text
    loaded last bits of sydh tfbs
  • lines changed 1, context: html, text, full: html, text
    changed windowsing function to mean+whiskers
  • lines changed 31, context: html, text, full: html, text
    changed t-rex-hek293 > hek293-t-rex and fetalpbde > pbdefetal
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.html
  • lines changed 10, context: html, text, full: html, text
    corrected some pre-QA errors
  • lines changed 49, context: html, text, full: html, text
    fixed html stuff and removed view settings from trackDb
  • lines changed 0, context: html, text, full: html, text
    html correction per QA request
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.ra
  • lines changed 1, context: html, text, full: html, text
    corrected some pre-QA errors
  • lines changed 7, context: html, text, full: html, text
    fixed html stuff and removed view settings from trackDb
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra
  • lines changed 619, context: html, text, full: html, text
    loaded new uw tracks
  • lines changed 2, context: html, text, full: html, text
    one of the rows was missing treatment
  • lines changed 2, context: html, text, full: html, text
    more treatment correction errors
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.ra
  • lines changed 361, context: html, text, full: html, text
    loaded new uw tracks
  • lines changed 9, context: html, text, full: html, text
    added one more submission 4696
  • lines changed 324, context: html, text, full: html, text
    something went wrong on the add last time
  • lines changed 36, context: html, text, full: html, text
    forgot treatment group
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
  • lines changed 171, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrRnaSeq.ra
  • lines changed 61, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
  • lines changed 186, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra
  • lines changed 1, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
  • lines changed 39, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 28, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhRnaSeq.ra
  • lines changed 10, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 259, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 341, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwRnaSeq.ra
  • lines changed 116, context: html, text, full: html, text
    added md5sums