File Changes for mspeir

v352_preview to v352_preview2 (2017-07-03 to 2017-07-10) v352

• python/lib/ucscGb/qa/tables/checkGapOverlap.py
  • lines changed 5, context: html, text, full: html, text
    c6266a24ec2f94547db8ce8109a4180800d41dae Thu Jun 29 14:17:03 2017 -0700
    Renaming tableTypeUtils to trackUtils as it more accurate. Also more track-centered functions will be added to it soon. Changing references to tableTypeUtils to trackUtils. Inspired by CR, refs #19495
  • lines changed 87, context: html, text, full: html, text
    a97ba306c1d4392680e93bd87e5ca2a90df64c7f Wed Jul 5 15:12:48 2017 -0700
    Improving output from constructOutputUrls function to be aware of parents, both composites and superTracks. Also changed checkGapOverlap function to call makeBedFromTable for gap tables. Putting functions from checkGapOverlap.py and positionalQa.py into trackUtils.py to make them more accessible. The trackUtils.py should contain a pretty side selection of generally applicable functions that operate on tracks (and tables). Most functions were unchanged after their move (outside of changing references to what were once outside functions). Two functions were improved: makeBedFromTable and getLabels. I made getLabels work on correctly getting parent labels for both superTrack and composites and (hopefully) any combination of the two. The function makeBedFromTable now has a 'whereOpt' parameter that allows you to add a where filter to the hgsql command. Changed some references to 'table' to 'track' to be more consistent (e.g. a function named getTrackType that had table as one of its parameters). Lastly, changed the checkLabelLengths function in positonalQa.py to use new getLabels function. All inspired by Chris Lee in a Code Review, refs #19495
• python/lib/ucscGb/qa/tables/factory.py
  • lines changed 6, context: html, text, full: html, text
    c6266a24ec2f94547db8ce8109a4180800d41dae Thu Jun 29 14:17:03 2017 -0700
    Renaming tableTypeUtils to trackUtils as it more accurate. Also more track-centered functions will be added to it soon. Changing references to tableTypeUtils to trackUtils. Inspired by CR, refs #19495
• python/lib/ucscGb/qa/tables/positionalQa.py
  • lines changed 2, context: html, text, full: html, text
    c6266a24ec2f94547db8ce8109a4180800d41dae Thu Jun 29 14:17:03 2017 -0700
    Renaming tableTypeUtils to trackUtils as it more accurate. Also more track-centered functions will be added to it soon. Changing references to tableTypeUtils to trackUtils. Inspired by CR, refs #19495
  • lines changed 35, context: html, text, full: html, text
    a97ba306c1d4392680e93bd87e5ca2a90df64c7f Wed Jul 5 15:12:48 2017 -0700
    Improving output from constructOutputUrls function to be aware of parents, both composites and superTracks. Also changed checkGapOverlap function to call makeBedFromTable for gap tables. Putting functions from checkGapOverlap.py and positionalQa.py into trackUtils.py to make them more accessible. The trackUtils.py should contain a pretty side selection of generally applicable functions that operate on tracks (and tables). Most functions were unchanged after their move (outside of changing references to what were once outside functions). Two functions were improved: makeBedFromTable and getLabels. I made getLabels work on correctly getting parent labels for both superTrack and composites and (hopefully) any combination of the two. The function makeBedFromTable now has a 'whereOpt' parameter that allows you to add a where filter to the hgsql command. Changed some references to 'table' to 'track' to be more consistent (e.g. a function named getTrackType that had table as one of its parameters). Lastly, changed the checkLabelLengths function in positonalQa.py to use new getLabels function. All inspired by Chris Lee in a Code Review, refs #19495
• python/lib/ucscGb/qa/tables/tableTypeUtils.py
  • lines changed 89, context: html, text, full: html, text
    c6266a24ec2f94547db8ce8109a4180800d41dae Thu Jun 29 14:17:03 2017 -0700
    Renaming tableTypeUtils to trackUtils as it more accurate. Also more track-centered functions will be added to it soon. Changing references to tableTypeUtils to trackUtils. Inspired by CR, refs #19495
• python/lib/ucscGb/qa/tables/trackUtils.py
  • lines changed 89, context: html, text, full: html, text
    c6266a24ec2f94547db8ce8109a4180800d41dae Thu Jun 29 14:17:03 2017 -0700
    Renaming tableTypeUtils to trackUtils as it more accurate. Also more track-centered functions will be added to it soon. Changing references to tableTypeUtils to trackUtils. Inspired by CR, refs #19495
  • lines changed 114, context: html, text, full: html, text
    a97ba306c1d4392680e93bd87e5ca2a90df64c7f Wed Jul 5 15:12:48 2017 -0700
    Improving output from constructOutputUrls function to be aware of parents, both composites and superTracks. Also changed checkGapOverlap function to call makeBedFromTable for gap tables. Putting functions from checkGapOverlap.py and positionalQa.py into trackUtils.py to make them more accessible. The trackUtils.py should contain a pretty side selection of generally applicable functions that operate on tracks (and tables). Most functions were unchanged after their move (outside of changing references to what were once outside functions). Two functions were improved: makeBedFromTable and getLabels. I made getLabels work on correctly getting parent labels for both superTrack and composites and (hopefully) any combination of the two. The function makeBedFromTable now has a 'whereOpt' parameter that allows you to add a where filter to the hgsql command. Changed some references to 'table' to 'track' to be more consistent (e.g. a function named getTrackType that had table as one of its parameters). Lastly, changed the checkLabelLengths function in positonalQa.py to use new getLabels function. All inspired by Chris Lee in a Code Review, refs #19495