angie: changes by file

review to branch (2009-11-17 to 2009-12-01) v220

• src/fuse/udcFuse/udcFuse.c
  • 1.6 lines changed: 39, context: html, text, full: html, text
    Path may now include http auth info (that's the only way of communicating the info to udcFuse) -- if so, strip it out when making the udc cache path.
  • 1.5 lines changed: 10, context: html, text, full: html, text
    Debug message improvements.
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.508 lines changed: 5, context: html, text, full: html, text
    Change bam cart variable names and bamTrack code to use Tim's cart and trackDb ClosestToHome API.
• src/hg/hgTracks/bamTrack.c
  • 1.18 lines changed: 46, context: html, text, full: html, text
    Change bam cart variable names and bamTrack code to use Tim's cart and trackDb ClosestToHome API.
  • 1.17 lines changed: 21, context: html, text, full: html, text
    Add pairSearchRange setting-controlled extra search for improperly paired items' mates that didn't happen to fall in the viewing window, a la hgc/bamClick.c.
  • 1.16 lines changed: 6, context: html, text, full: html, text
    Needed to be a bit more careful setting both stub coordinates and lfs->end -- was getting lfs->end too short, resulting in too short cachedDna in cds.c in some cases.
• src/hg/hgc/bamClick.c
  • 1.12 lines changed: 18, context: html, text, full: html, text
    Refinements to searching for mates out of window: don't do the extra bamFetch unless pairSearchRange > 0; increase default pairSearchRange default; clip start of window at 0; there's only one item name, so don't need to loop on pairHash name.
• src/hg/lib/bamFile.c
  • 1.16 lines changed: 28, context: html, text, full: html, text
    Since samtools' bam_index_load saves .bai files to the current directory, change to a trashDir when calling it (instead of using a locally hacked samtools).
  • 1.15 lines changed: 5, context: html, text, full: html, text
    Include http auth string in udcFuse path because udcFuse has no other way to get the auth.
• src/hg/lib/cart.c
  • 1.113 lines changed: 1, context: html, text, full: html, text
    Adding more const qualifiers because cart.c needs startsWith and wildMatch to have the same signature (thanks Galt!).
• src/hg/lib/wiggleCart.c
  • 1.30 lines changed: 1, context: html, text, full: html, text
    Display wigFetchMinMaxYWithCart's warning about missing data range settings only when we're on hgwdev.
  • 1.29 lines changed: 20, context: html, text, full: html, text
    Removed the clipping of viewing range to (optionally expanded) data range at Jim's request. Since that removes the purpose of expanding the data range to viewLimits or settingsByView's viewLimitsMax, I took that out too and those trackDb settings are now ignored & obsolete.
  • 1.28 lines changed: 3, context: html, text, full: html, text
    Oops, logic bug prevented absMin from being set properly for wiggle (thanks again Jim!)
  • 1.27 lines changed: 1, context: html, text, full: html, text
    Oops, used double instead of int for abs{Min,Max} -- thanks Jim!
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.431 lines changed: 24, context: html, text, full: html, text
    Turned bamNA12878 into a subtrack of a new composite track that includes bamNA12891 as well. Adding experimental track phasedGenotypesNA12878 (looks like trivial phasing, but still maybe of interest).
• src/hg/near/hgNear/hgNear.c
  • 1.185 lines changed: 6, context: html, text, full: html, text
    Removing duplicate definition of anyWild (use the common.h/wildcmp.c version).
• src/hg/near/hgNear/hgNear.h
  • 1.99 lines changed: 3, context: html, text, full: html, text
    Removing duplicate definition of anyWild (use the common.h/wildcmp.c version).
• src/inc/common.h
  • 1.161 lines changed: 2, context: html, text, full: html, text
    Adding more const qualifiers because cart.c needs startsWith and wildMatch to have the same signature (thanks Galt!).
  • 1.160 lines changed: 1, context: html, text, full: html, text
    Added a couple const keywords for smoother interoperation with external code.
• src/inc/udc.h
  • 1.17 lines changed: 3, context: html, text, full: html, text
    Added udcParseUrlFull, which returns http auth portion instead of silently skipping it.
• src/lib/common.c
  • 1.137 lines changed: 1, context: html, text, full: html, text
    Added a couple const keywords for smoother interoperation with external code.
• src/lib/udc.c
  • 1.30 lines changed: 19, context: html, text, full: html, text
    Added udcParseUrlFull, which returns http auth portion instead of silently skipping it.
  • 1.29 lines changed: 2, context: html, text, full: html, text
    Adding rcsid for version tracking with ident.
  • 1.28 lines changed: 4, context: html, text, full: html, text
    Fix: remember to close sockets if necessary in udcFileClose.
• src/lib/wildcmp.c
  • 1.7 lines changed: 4, context: html, text, full: html, text
    Adding more const qualifiers because cart.c needs startsWith and wildMatch to have the same signature (thanks Galt!).