Commits for cline

v251_base to v252_preview (2011-05-10 to 2011-05-17) v252

• Changing the case of human and mouse, so that the validation will work
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 2, context: html, text, full: html, text
• changed the mouse stanza to type organism, as it should've been
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text
• Added a new script to parse new antibody registrations out of the wiki, and download any new, approved validation documents
  • src/hg/encode/antibodyWikiParser.py - lines changed 272, context: html, text, full: html, text
• Added three new antibodies. Changed the case of the organism Human and Mouse in various places, to facilitate validation
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 107, context: html, text, full: html, text
• Fixed a bug involving removing double-soft edges that are embedded in a double-hard or half-hard edge. The range tree that was collecting the ranges of hard edges contained a pointer to only the edge added most recently. When a double soft was found that fell within the range, it was merged with the edge for the range. The problem was that the coordinates of the edge might be a subset of the coordinates of the range. So, when the evidence for the double-soft edge was assigned to the range, it was potentially assigned to an edge that it didn't overlap. To address this, in the range nodes, I'm collecting a singly-linked list of all candidate hard edges. When a double soft is found to fall within a range, I look for a single edge that it falls within. If I find such an edge, then I reassign the evidence
  • src/hg/txGraph/txBedToGraph/makeGraph.c - lines changed 72, context: html, text, full: html, text
• Post code review check-in. This includes a huge number of changes, based on incorporating the NHGRI-curated spreadsheet modifications, as entered by Cricket and reviewed by Jeff
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 410, context: html, text, full: html, text
• Back-filled the age and strain in mouse tissues to Unknown, as appropriate, so that the lack of age or strain won't be tagged by the validator
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 115, context: html, text, full: html, text
• Added PMID links to satisfy Redmine # 2711
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 29, context: html, text, full: html, text
• Back-filled the order URLs for several mouse tissue entries, for validation purposes. These are mouse cell types that are produced within the lab, and the order URL is essentially the lab itself
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 69, context: html, text, full: html, text