All File Changes

v242_preview to v242_base (2010-10-05 to 2010-10-12) v242

• src/hg/bedIntersect/bedIntersect.c
  • lines changed 5, context: html, text, full: html, text
    Added -tab option to bedIntersect (chopping by spaces, printing out w/tabs caused incorrect column counts).
  • lines changed 132, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/makefile
  • lines changed 5, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAny.aBigBSub.bed
  • lines changed 1, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAny.aSubBBig.bed
  • lines changed 7, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusBScore.aBigBSub.bed
  • lines changed 1, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusBScore.aSubBBig.bed
  • lines changed 7, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusBScorePlusMinCov.aBigBSub.10.bed
  • lines changed 1, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusBScorePlusMinCov.aBigBSub.10.stderr
  • lines changed 1, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusBScorePlusMinCov.aBigBSub.100.bed
  • lines changed 1, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusBScorePlusMinCov.aBigBSub.100.stderr
  • lines changed 6, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusBScorePlusMinCov.aBigBSub.5.bed
  • lines changed 1, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusBScorePlusMinCov.aBigBSub.5.stderr
  • lines changed 0, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusBScorePlusMinCov.aBigBSub.50.bed
  • lines changed 1, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusBScorePlusMinCov.aBigBSub.50.stderr
  • lines changed 5, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusBScorePlusMinCov.aSubBBig.10.bed
  • lines changed 7, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusBScorePlusMinCov.aSubBBig.10.stderr
  • lines changed 0, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusBScorePlusMinCov.aSubBBig.100.bed
  • lines changed 5, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusBScorePlusMinCov.aSubBBig.100.stderr
  • lines changed 2, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusBScorePlusMinCov.aSubBBig.5.bed
  • lines changed 7, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusBScorePlusMinCov.aSubBBig.5.stderr
  • lines changed 0, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusBScorePlusMinCov.aSubBBig.50.bed
  • lines changed 7, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusBScorePlusMinCov.aSubBBig.50.stderr
  • lines changed 0, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusMinCov.aBigBSub.10.bed
  • lines changed 1, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusMinCov.aBigBSub.10.stderr
  • lines changed 1, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusMinCov.aBigBSub.100.bed
  • lines changed 1, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusMinCov.aBigBSub.100.stderr
  • lines changed 6, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusMinCov.aBigBSub.5.bed
  • lines changed 1, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusMinCov.aBigBSub.5.stderr
  • lines changed 0, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusMinCov.aBigBSub.50.bed
  • lines changed 1, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusMinCov.aBigBSub.50.stderr
  • lines changed 5, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusMinCov.aSubBBig.10.bed
  • lines changed 7, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusMinCov.aSubBBig.10.stderr
  • lines changed 0, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusMinCov.aSubBBig.100.bed
  • lines changed 5, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusMinCov.aSubBBig.100.stderr
  • lines changed 2, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusMinCov.aSubBBig.5.bed
  • lines changed 7, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusMinCov.aSubBBig.5.stderr
  • lines changed 0, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusMinCov.aSubBBig.50.bed
  • lines changed 7, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/aHitAnyPlusMinCov.aSubBBig.50.stderr
  • lines changed 0, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/allowStartEqEnd.aBigBSub.bed
  • lines changed 10, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/allowStartEqEnd.aSubBBig.bed
  • lines changed 10, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/allowStartEqEndPlusAHitAny.aBigBSub.bed
  • lines changed 1, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/allowStartEqEndPlusAHitAny.aSubBBig.bed
  • lines changed 10, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/allowStartEqEndPlusAHitAnyPlusBScore.aBigBSub.bed
  • lines changed 1, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/allowStartEqEndPlusAHitAnyPlusBScore.aSubBBig.bed
  • lines changed 10, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/bScore.aBigBSub.bed
  • lines changed 7, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/bScore.aSubBBig.bed
  • lines changed 7, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/bScorePlusMinCov.aBigBSub.10.bed
  • lines changed 7, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/bScorePlusMinCov.aBigBSub.100.bed
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    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/bScorePlusMinCov.aBigBSub.5.bed
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    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/bScorePlusMinCov.aBigBSub.50.bed
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    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/bScorePlusMinCov.aSubBBig.10.bed
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    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/bScorePlusMinCov.aSubBBig.100.bed
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    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/bScorePlusMinCov.aSubBBig.5.bed
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    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/bScorePlusMinCov.aSubBBig.50.bed
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    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/default.aBigBSub.bed
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    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/default.aSubBBig.bed
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    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/minCov.aBigBSub.10.bed
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    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/minCov.aBigBSub.100.bed
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    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/minCov.aBigBSub.5.bed
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    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/minCov.aBigBSub.50.bed
  • lines changed 7, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/minCov.aSubBBig.10.bed
  • lines changed 4, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/minCov.aSubBBig.100.bed
  • lines changed 1, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/minCov.aSubBBig.5.bed
  • lines changed 6, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/expected/minCov.aSubBBig.50.bed
  • lines changed 2, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/input/bigBlock.bed
  • lines changed 1, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/input/subBlocks.bed
  • lines changed 21, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/bedIntersect/tests/makefile
  • lines changed 120, context: html, text, full: html, text
    Redmine Track #1261 (Construct track of "bad apple" coverage anomalies in human genome): Added -allowStartEqualEnd (as in hgLoadBed) so that 0-length items like insertions aren't lost -- Mary-Claire King pointed out the lack of insertions in the first version of the track, oops. Majorly refactored bedIntersect.c and added test cases.
• src/hg/encode/encodeMkGeoPkg/README.txt
  • lines changed 1, context: html, text, full: html, text
    Added Path for aspera to instructions
• src/hg/encode/encodeMkGeoPkg/encodeMkGeoPkg
  • lines changed 4, context: html, text, full: html, text
    Added line to warn that file was genereted by DCC and is not submitted to GEO
  • lines changed 3, context: html, text, full: html, text
    fixed the protocol link to include the organism in the path
  • lines changed 4, context: html, text, full: html, text
    GEO changes
• src/hg/encode/encodeValidate/config/cv.ra
  • lines changed 18, context: html, text, full: html, text
    Adding tags to grant entries
  • lines changed 65, context: html, text, full: html, text
    Added labels to labs for cleaner findTracks display. Labs still need cleanup in mdb and cv.ra
  • lines changed 17, context: html, text, full: html, text
    Added Cell line SK-SY5Y and protocol
  • lines changed 17, context: html, text, full: html, text
    actually added SH-SY5Y this time...
• src/hg/encode/geoSofts/ucsc_encode_dcc_wgEncodeCshlShortRnaSeq.soft
  • lines changed 339, context: html, text, full: html, text
    Soft File for CSHL Short RNA-seq, submission for GEO.
• src/hg/encode/hgEncodeDataVersions/hgEncodeDataVersions.c
  • lines changed 1, context: html, text, full: html, text
    eliminate the chrom argument from function hTrackDb() in hdb.c
• src/hg/encode/hgEncodeSubmit/pipeline_runner.rb
  • lines changed 4, context: html, text, full: html, text
    adding some juicy comments
  • lines changed 8, context: html, text, full: html, text
    added elsif
• src/hg/encode/metaCheck/metaCheck.c
  • lines changed 3, context: html, text, full: html, text
    check for fileName's in blocks even if the type is not file
• src/hg/encode/metaCollect/metaCollect.c
  • lines changed 59, context: html, text, full: html, text
    more stuff, not finished
• src/hg/encode/validateFiles/validateFiles.c
  • lines changed 130, context: html, text, full: html, text
    bam percentages, show bad aligns, check quality length in fastq
• src/hg/hgApi/hgApi.c
  • lines changed 6, context: html, text, full: html, text
    mdb val dropdown now shows cv.ra 'label' instead of val if one exists.
  • lines changed 1, context: html, text, full: html, text
    eliminate the chrom argument from function hTrackDb() in hdb.c
• src/hg/hgGateway/hgGateway.c
  • lines changed 1, context: html, text, full: html, text
    Make cgi references to style sheets (css files) actually point to timestamped link. Common code is also used for js files
• src/hg/hgGenome/import.c
  • lines changed 1, context: html, text, full: html, text
    eliminate the chrom argument from function hTrackDb() in hdb.c
• src/hg/hgKnownGeneList/hgKnownGeneList.c
  • lines changed 7, context: html, text, full: html, text
    Make cgi references to style sheets (css files) actually point to timestamped link. Common code is also used for js files
• src/hg/hgTables/bedList.c
  • lines changed 33, context: html, text, full: html, text
    cache calls to hTrackDbForTrack and hFindTableInfo to fix slow queries on contig-based assemblies
  • lines changed 33, context: html, text, full: html, text
    trying a cache of loadTrackDb result
• src/hg/hgTables/hgTables.c
  • lines changed 1, context: html, text, full: html, text
    eliminate the chrom argument from function hTrackDb() in hdb.c
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 1, context: html, text, full: html, text
    Make cgi references to style sheets (css files) actually point to timestamped link. Common code is also used for js files
• src/hg/hgTracks/altGraphXTrack.c
  • lines changed 2, context: html, text, full: html, text
    Added some missing hFreeConn's and removed one dead-code hFreeConn.
• src/hg/hgTracks/bamTrack.c
  • lines changed 44, context: html, text, full: html, text
    Branched first cut at Redmine Feature #1093 (BAM: range settings foralignment quality and base quality). I think it works, will test more before merging and pushing.
  • lines changed 3, context: html, text, full: html, text
    Tweaked a comment to finish work on Redmine Feature #1093.
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    eliminate the chrom argument from function hTrackDb() in hdb.c
  • lines changed 3, context: html, text, full: html, text
    Make cgi references to style sheets (css files) actually point to timestamped link. Common code is also used for js files
• src/hg/hgTracks/mainMain.c
  • lines changed 1, context: html, text, full: html, text
    Added paging to findTracks and icons to findTracks and icons
  • lines changed 5, context: html, text, full: html, text
    Make cgi references to style sheets (css files) actually point to timestamped link. Common code is also used for js files
• src/hg/hgTracks/searchTracks.c
  • lines changed 100, context: html, text, full: html, text
    Added paging to findTracks and icons to findTracks and icons
  • lines changed 26, context: html, text, full: html, text
    mdb val dropdown now shows cv.ra 'label' instead of val if one exists.
  • lines changed 1, context: html, text, full: html, text
    Added some missing hFreeConn's and removed one dead-code hFreeConn.
  • lines changed 1, context: html, text, full: html, text
    Swapped 'geoSample' for 'accession' as a whitelisted term
  • lines changed 23, context: html, text, full: html, text
    Removed some ifdefs
• src/hg/hgTracks/simpleTracks.c
  • lines changed 2, context: html, text, full: html, text
    Added some missing hFreeConn's and removed one dead-code hFreeConn.
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    eliminate the chrom argument from function hTrackDb() in hdb.c
  • lines changed 1, context: html, text, full: html, text
    Make cgi references to style sheets (css files) actually point to timestamped link. Common code is also used for js files
  • lines changed 7, context: html, text, full: html, text
    adding blastCe9SG business, this should be done from trackDb variables ...
  • lines changed 2, context: html, text, full: html, text
    some punctuation at r-head's request
• src/hg/htdocs/goldenPath/help/image.html
  • lines changed 54, context: html, text, full: html, text
    explanation for how to reload browser page
  • lines changed 2, context: html, text, full: html, text
    typo
  • lines changed 1, context: html, text, full: html, text
    one more tweak
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 2, context: html, text, full: html, text
    Changed links to abstract versions for 2 pubs.
• src/hg/htdocs/images/book.png
  • lines changed 0, context: html, text, full: html, text
    Added some icons
• src/hg/htdocs/images/bookOut.png
  • lines changed 0, context: html, text, full: html, text
    One more icon
• src/hg/htdocs/images/dnaIcon.png
  • lines changed 0, context: html, text, full: html, text
    Added some icons
• src/hg/htdocs/images/folderWrench.png
  • lines changed 0, context: html, text, full: html, text
    Added some icons
• src/hg/htdocs/images/magnify.png
  • lines changed 0, context: html, text, full: html, text
    Added some icons
• src/hg/htdocs/images/toggle.png
  • lines changed 0, context: html, text, full: html, text
    Added some icons
• src/hg/htdocs/images/view.png
  • lines changed 0, context: html, text, full: html, text
    Added some icons
• src/hg/htdocs/images/wrench.png
  • lines changed 0, context: html, text, full: html, text
    Added some icons
• src/hg/htdocs/makefile
  • lines changed 3, context: html, text, full: html, text
    calling style make automatically for targets user alpha beta
• src/hg/htdocs/style/cpAndLinkToResourceFiles.pl
  • lines changed 94, context: html, text, full: html, text
    Added makefile and make install to create timestamped links for css files
• src/hg/htdocs/style/makefile
  • lines changed 28, context: html, text, full: html, text
    Added makefile and make install to create timestamped links for css files
  • lines changed 8, context: html, text, full: html, text
    Updated Makefile to accomadate user specific htdocs style directories
• src/hg/inc/hdb.h
  • lines changed 7, context: html, text, full: html, text
    eliminate the chrom argument from function hTrackDb() in hdb.c
• src/hg/inc/mdb.h
  • lines changed 5, context: html, text, full: html, text
    Expanded mdbValSearch to mdbValLabelSearch which will swap a cv.ra label if one exists
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v242
• src/hg/inc/web.h
  • lines changed 15, context: html, text, full: html, text
    Make cgi references to style sheets (css files) actually point to timestamped link. Common code is also used for js files
• src/hg/js/hgTracks.js
  • lines changed 30, context: html, text, full: html, text
    Added paging to findTracks and icons to findTracks and icons
  • lines changed 15, context: html, text, full: html, text
    suppress help links for metadata items which have no detailed help
  • lines changed 3, context: html, text, full: html, text
    mdb val dropdown now shows cv.ra 'label' instead of val if one exists.
  • lines changed 1, context: html, text, full: html, text
    IE Doesn't like the extra comma
  • lines changed 2, context: html, text, full: html, text
    disable some more help links
  • lines changed 5, context: html, text, full: html, text
    Black listed a couple more mdb vars from having help links
  • lines changed 22, context: html, text, full: html, text
    add windowOpenFailedMsg; don't put 'Click to alter ...' items in the contextmenu
• src/hg/js/hui.js
  • lines changed 1, context: html, text, full: html, text
    Added paging to findTracks and icons to findTracks and icons
• src/hg/js/jquery.contextmenu.js
  • lines changed 1, context: html, text, full: html, text
    minor comment
  • lines changed 4, context: html, text, full: html, text
    add in 1.1 changes from plugin website
• src/hg/lib/hdb.c
  • lines changed 13, context: html, text, full: html, text
    trying a cache of loadTrackDb result
  • lines changed 9, context: html, text, full: html, text
    eliminate the chrom argument from function hTrackDb() in hdb.c
  • lines changed 1, context: html, text, full: html, text
    there are no calls to hTrackDb(NULL) except in obsolete hgText.c
  • lines changed 8, context: html, text, full: html, text
    back out the hTrackDb caching, doesn't work
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    eliminate the chrom argument from function hTrackDb() in hdb.c
  • lines changed 2, context: html, text, full: html, text
    Make cgi references to style sheets (css files) actually point to timestamped link. Common code is also used for js files
• src/hg/lib/jsHelper.c
  • lines changed 84, context: html, text, full: html, text
    Make cgi references to style sheets (css files) actually point to timestamped link. Common code is also used for js files
• src/hg/lib/mdb.c
  • lines changed 70, context: html, text, full: html, text
    Expanded mdbValSearch to mdbValLabelSearch which will swap a cv.ra label if one exists
  • lines changed 3, context: html, text, full: html, text
    Fixed the sort on mdbValLabelSearch
  • lines changed 7, context: html, text, full: html, text
    Special case for labs which are case insensitive. Need case insensitive hashing.
• src/hg/lib/rgdGeneRaw0.sql
  • lines changed 1, context: html, text, full: html, text
    Initial check in of RGD Genes build.
• src/hg/lib/rgdGeneRaw2cds.sql
  • lines changed 12, context: html, text, full: html, text
    Initial check in of RGD Genes build.
• src/hg/lib/rgdGeneRaw2exon.sql
  • lines changed 12, context: html, text, full: html, text
    Initial check in of RGD Genes build.
• src/hg/lib/rgdGeneRaw2gene.sql
  • lines changed 12, context: html, text, full: html, text
    Initial check in of RGD Genes build.
• src/hg/lib/searchTracks.c
  • lines changed 3, context: html, text, full: html, text
    Trix is in /gbdb/ so must have separate name for beta version in order to avoid beta stepping on RR. This is done by a different name for the beta files and an hg.conf setting for beta.
• src/hg/lib/trackDb.c
  • lines changed 6, context: html, text, full: html, text
    these free operations are currently dangerous with cached tdb
  • lines changed 4, context: html, text, full: html, text
    back out the hTrackDb caching, doesn't work
• src/hg/lib/web.c
  • lines changed 131, context: html, text, full: html, text
    Make cgi references to style sheets (css files) actually point to timestamped link. Common code is also used for js files
• src/hg/makeDb/doc/bruMal1.txt
  • lines changed 177, context: html, text, full: html, text
    done with blastCe9SG ce9 sangerGene tblastn
  • lines changed 8, context: html, text, full: html, text
    done with all 9 tblastn.ce9SG
• src/hg/makeDb/doc/caeJap3.txt
  • lines changed 180, context: html, text, full: html, text
    done with all 9 tblastn.ce9SG
• src/hg/makeDb/doc/caePb2.txt
  • lines changed 181, context: html, text, full: html, text
    done with all 9 tblastn.ce9SG
• src/hg/makeDb/doc/caeRem3.txt
  • lines changed 175, context: html, text, full: html, text
    done with blastCe9SG ce9 sangerGene tblastn
  • lines changed 12, context: html, text, full: html, text
    done with all 9 tblastn.ce9SG
• src/hg/makeDb/doc/cb3.txt
  • lines changed 178, context: html, text, full: html, text
    done with blastCe9SG ce9 sangerGene tblastn
  • lines changed 16, context: html, text, full: html, text
    done with all 9 tblastn.ce9SG
• src/hg/makeDb/doc/ce9.txt
  • lines changed 274, context: html, text, full: html, text
    reworked priPac1 to be priPac2 in the 10-way and working on phastCons
  • lines changed 175, context: html, text, full: html, text
    done with phastCons starting on phyloP for 10-way
• src/hg/makeDb/doc/haeCon1.txt
  • lines changed 179, context: html, text, full: html, text
    done with all 9 tblastn.ce9SG
• src/hg/makeDb/doc/hg18.txt
  • lines changed 139, context: html, text, full: html, text
    Added subtracks to 1000 Genomes coverage-masking: unions across populations & masking types (Redmine Track #1079). Intersected the union subtracks with snp130 to make 'bad apples' tracks requested by Mary-Claire King (Redmine Track #1261). The 'bad apples' tracks need a new name and a description still, but the data are under review by MCK and colleagues.
  • lines changed 6, context: html, text, full: html, text
    Updated gwasCatalog in hg18 and hg19.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 3, context: html, text, full: html, text
    Updated gwasCatalog in hg18 and hg19.
  • lines changed 5, context: html, text, full: html, text
    Done affyU95
• src/hg/makeDb/doc/melHap1.txt
  • lines changed 173, context: html, text, full: html, text
    done with blastCe9SG ce9 sangerGene tblastn
  • lines changed 12, context: html, text, full: html, text
    done with all 9 tblastn.ce9SG
• src/hg/makeDb/doc/melInc1.txt
  • lines changed 173, context: html, text, full: html, text
    done with blastCe9SG ce9 sangerGene tblastn
  • lines changed 12, context: html, text, full: html, text
    done with all 9 tblastn.ce9SG
• src/hg/makeDb/doc/mm9.txt
  • lines changed 2, context: html, text, full: html, text
    Removing redundant chomp's noticed by Belinda in code review.
• src/hg/makeDb/doc/priPac2.txt
  • lines changed 179, context: html, text, full: html, text
    done with all 9 tblastn.ce9SG
• src/hg/makeDb/doc/rn4.txt
  • lines changed 140, context: html, text, full: html, text
    Initial check in of RGD Genes build.
• src/hg/makeDb/trackDb/README
  • lines changed 4, context: html, text, full: html, text
    Branched first cut at Redmine Feature #1093 (BAM: range settings foralignment quality and base quality). I think it works, will test more before merging and pushing.
• src/hg/makeDb/trackDb/buildTrix
  • lines changed 46, context: html, text, full: html, text
    build the TRIX index for the track search tool
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeBuOrchid.ra
  • lines changed 3, context: html, text, full: html, text
    dataType change
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 846, context: html, text, full: html, text
    Changing dataType, view and accession in metaDb
  • lines changed 1, context: html, text, full: html, text
    got the magic number this time
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeChromatinMap.ra
  • lines changed 474, context: html, text, full: html, text
    Changing dataType, view and accession in metaDb
  • lines changed 6, context: html, text, full: html, text
    UT-Austin to UT-A
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 26, context: html, text, full: html, text
    LongRnaSeq to RnaSeq
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 39, context: html, text, full: html, text
    Added GEO Sample and Series information to meta-data
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeGisPet.ra
  • lines changed 129, context: html, text, full: html, text
    Changing dataType, view and accession in metaDb
  • lines changed 4, context: html, text, full: html, text
    removed accession entirely
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaMethyl27.ra
  • lines changed 7, context: html, text, full: html, text
    Changing dataType, view and accession in metaDb
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaRnaSeq.ra
  • lines changed 7, context: html, text, full: html, text
    Changing dataType, view and accession in metaDb
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 2, context: html, text, full: html, text
    Changing dataType, view and accession in metaDb
  • lines changed 2, context: html, text, full: html, text
    removed accession entirely
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeSangerGencode.ra
  • lines changed 4, context: html, text, full: html, text
    Changing dataType, view and accession in metaDb
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwChIPSeq.ra
  • lines changed 562, context: html, text, full: html, text
    Changing dataType, view and accession in metaDb
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwDGF.ra
  • lines changed 29, context: html, text, full: html, text
    got the magic number this time
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwDnaseSeq.ra
  • lines changed 2, context: html, text, full: html, text
    one more accession wrong
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleChIPseq.ra
  • lines changed 5, context: html, text, full: html, text
    Removed GEO Series information from labVersion and added it to accession for 2 objects
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleRNAseq.ra
  • lines changed 31, context: html, text, full: html, text
    More dataType changes
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    preparing for metaDb release
  • lines changed 1, context: html, text, full: html, text
    adding wgEncodeGisPet.ra to the makefile to stage on beta
  • lines changed 1, context: html, text, full: html, text
    staging metaDb on beta for wgEncodeHudsonalphaMethyl27.ra with recent changes from clean-up
  • lines changed 1, context: html, text, full: html, text
    staging wgEncodeHudsonalphaRnaSeq metaDb on beta with changes from metadata clean-up
  • lines changed 1, context: html, text, full: html, text
    staging wgEncodeRikenCage metaDb on beta with changes from metadata clean-up
  • lines changed 1, context: html, text, full: html, text
    staging wgEncodeSangerGencode metaDb on beta with changes from metadata clean-up
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeBuOrchid.ra
  • lines changed 35, context: html, text, full: html, text
    switching from trackDb metadata to metaDb metadata
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeChromatinMap.ra
  • lines changed 479, context: html, text, full: html, text
    staging metadata clean-up on beta
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeGisPet.ra
  • lines changed 2308, context: html, text, full: html, text
    staging metaDb, inlcuding recent changes resulting from clean-up on beta
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeHudsonalphaMethyl27.ra
  • lines changed 97, context: html, text, full: html, text
    staging metaDb on beta for wgEncodeHudsonalphaMethyl27.ra with recent changes from clean-up
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeHudsonalphaRnaSeq.ra
  • lines changed 279, context: html, text, full: html, text
    staging wgEncodeHudsonalphaRnaSeq metaDb on beta with changes from metadata clean-up
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeRikenCage.ra
  • lines changed 1439, context: html, text, full: html, text
    staging wgEncodeRikenCage metaDb on beta with changes from metadata clean-up
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeSangerGencode.ra
  • lines changed 55, context: html, text, full: html, text
    staging wgEncodeSangerGencode metaDb on beta with changes from metadata clean-up
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    preparing for metaDb release
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeBuOrchid.ra
  • lines changed 35, context: html, text, full: html, text
    preparing for metaDb release
• src/hg/makeDb/trackDb/human/hg18/numtSeq.html
  • lines changed 46, context: html, text, full: html, text
    Final html/name touch up
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    Removed rfamHuman, which is superseded by rfamConsensus on a development branch
  • lines changed 15, context: html, text, full: html, text
    Final html/name touch up
  • lines changed 35, context: html, text, full: html, text
    Added subtracks to 1000 Genomes coverage-masking: unions across populations & masking types (Redmine Track #1079). Intersected the union subtracks with snp130 to make 'bad apples' tracks requested by Mary-Claire King (Redmine Track #1261). The 'bad apples' tracks need a new name and a description still, but the data are under review by MCK and colleagues.
  • lines changed 18, context: html, text, full: html, text
    cactusBed and cactusMaf... helping Benedict and Ngan
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 451, context: html, text, full: html, text
    new submissions added
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
  • lines changed 1409, context: html, text, full: html, text
    new submissions added
  • lines changed 119, context: html, text, full: html, text
    subs 2118 and 2120 were stomping each other and now I think I have it fixed
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
  • lines changed 305, context: html, text, full: html, text
    Added missing metadata for submissions 1220 and 1221
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra
  • lines changed 2129, context: html, text, full: html, text
    new track, new metaDb.ra
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeYaleRnaSeq.ra
  • lines changed 210, context: html, text, full: html, text
    new submissions added
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    changed transfrag score min to 0 by default
  • lines changed 2, context: html, text, full: html, text
    removed scoreMin 0 for transfrags (didn't do anything & couldn't find it in the README), change scoreFilter from 100 to 0 so that the min transfrag displayed by default is 0
  • lines changed 1, context: html, text, full: html, text
    oops! the scoreMin sets the min score for the GrayLevel coloring, reinstated it
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra
  • lines changed 181, context: html, text, full: html, text
    new tracks
  • lines changed 120, context: html, text, full: html, text
    removed reference to K562 Chrom, Nulc, Nlos Pap as it should be Total
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.ra
  • lines changed 12, context: html, text, full: html, text
    label changes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.html
  • lines changed 98, context: html, text, full: html, text
    Updated track Description.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeYaleRnaSeq.ra
  • lines changed 59, context: html, text, full: html, text
    new track
• src/hg/makeDb/trackDb/human/trackDb.nt.ra
  • lines changed 1, context: html, text, full: html, text
    Branched first cut at Redmine Feature #1093 (BAM: range settings foralignment quality and base quality). I think it works, will test more before merging and pushing.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 44, context: html, text, full: html, text
    Added subtracks to 1000 Genomes coverage-masking: unions across populations & masking types (Redmine Track #1079). Intersected the union subtracks with snp130 to make 'bad apples' tracks requested by Mary-Claire King (Redmine Track #1261). The 'bad apples' tracks need a new name and a description still, but the data are under review by MCK and colleagues.
• src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
  • lines changed 13, context: html, text, full: html, text
    Initial check in of RGD Genes build.
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 2, context: html, text, full: html, text
    Branched first cut at Redmine Feature #1093 (BAM: range settings foralignment quality and base quality). I think it works, will test more before merging and pushing.
• src/hg/makeDb/trackDb/trackDb.nt.ra
  • lines changed 2, context: html, text, full: html, text
    Branched first cut at Redmine Feature #1093 (BAM: range settings foralignment quality and base quality). I think it works, will test more before merging and pushing.
• src/hg/makeDb/trackDb/worm/ce9/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    priPac1 has become priPac2
  • lines changed 9, context: html, text, full: html, text
    adjust priorities on the 10-way tracks and now displaying phastCons both graphs and first phyloP
  • lines changed 3, context: html, text, full: html, text
    done with 10-way alignment
• src/hg/makeDb/trackDb/worm/trackDb.ra
  • lines changed 19, context: html, text, full: html, text
    adding blastCe9SG
• src/hg/oneShot/doRgdGene2UniProt/doRgdGene2UniProt.c
  • lines changed 82, context: html, text, full: html, text
    Added a oneShot program for RGD Genes build.
• src/hg/oneShot/doRgdGene2UniProt/makefile
  • lines changed 38, context: html, text, full: html, text
    Added a oneShot program for RGD Genes build.
• src/hg/sageVisCGI/sageVisCGI.c
  • lines changed 1, context: html, text, full: html, text
    Make cgi references to style sheets (css files) actually point to timestamped link. Common code is also used for js files
• src/hg/utils/makeTrackIndex/makeTrackIndex.c
  • lines changed 1, context: html, text, full: html, text
    eliminate the chrom argument from function hTrackDb() in hdb.c
  • lines changed 14, context: html, text, full: html, text
    add more arguments to specify the metaDb and cv.ra locations
• src/hg/utils/makeTrackIndex/makefile
  • lines changed 10, context: html, text, full: html, text
    Trix is in /gbdb/ so must have separate name for beta version in order to avoid beta stepping on RR. This is done by a different name for the beta files and an hg.conf setting for beta.
• src/hg/visiGene/hgVisiGene/hgVisiGene.c
  • lines changed 3, context: html, text, full: html, text
    Make cgi references to style sheets (css files) actually point to timestamped link. Common code is also used for js files
• src/inc/common.h
  • lines changed 9, context: html, text, full: html, text
    Needed to sort slPair
• src/lib/common.c
  • lines changed 23, context: html, text, full: html, text
    Needed to sort slPair
• src/lib/memalloc.c
  • lines changed 1, context: html, text, full: html, text
    identify source of alloc error
• src/utils/qa/weeklybld/buildBeta.csh
  • lines changed 16, context: html, text, full: html, text
    adding make alpha in hg/htdocs to bi-weekly build
  • lines changed 16, context: html, text, full: html, text
    Revert "adding make alpha in hg/htdocs to bi-weekly build" More discussion is needed. This reverts commit bb4ca2a9ea65672b4e828c9a2dac3f0d381f1e6f.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v242 final build
• src/utils/qa/weeklybld/doNewReview.csh
  • lines changed 1, context: html, text, full: html, text
    fixing comment

• lines changed: 17094
• files changed: 257