angie: changes by commit
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review to branch (2009-11-17 to 2009-12-01) v220
- Oops, used double instead of int for abs{Min,Max} -- thanks Jim!
- src/hg/lib/wiggleCart.c 1.27 - lines changed: 1, context: html, text, full: html, text
- Oops, logic bug prevented absMin from being set properly for wiggle (thanks again Jim!)
- src/hg/lib/wiggleCart.c 1.28 - lines changed: 3, 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.
- src/hg/lib/wiggleCart.c 1.29 - lines changed: 20, context: html, text, full: html, text
- Debug message improvements.
- src/fuse/udcFuse/udcFuse.c 1.5 - lines changed: 10, context: html, text, full: html, text
- Fix: remember to close sockets if necessary in udcFileClose.
- Adding rcsid for version tracking with ident.
- Added a couple const keywords for smoother interoperation with external code.
- src/inc/common.h 1.160 - lines changed: 1, context: html, text, full: html, text
- src/lib/common.c 1.137 - lines changed: 1, context: html, text, full: html, text
- Added udcParseUrlFull, which returns http auth portion instead of silently skipping it.
- Include http auth string in udcFuse path because udcFuse has no other way to get the auth.
- src/hg/lib/bamFile.c 1.15 - lines changed: 5, 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.
- src/fuse/udcFuse/udcFuse.c 1.6 - lines changed: 39, 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/cart.c 1.113 - lines changed: 1, context: html, text, full: html, text
- src/inc/common.h 1.161 - lines changed: 2, context: html, text, full: html, text
- src/lib/wildcmp.c 1.7 - lines changed: 4, context: html, text, full: html, text
- Removing duplicate definition of anyWild (use the common.h/wildcmp.c version).
- src/hg/near/hgNear/hgNear.c 1.185 - lines changed: 6, context: html, text, full: html, text
- src/hg/near/hgNear/hgNear.h 1.99 - lines changed: 3, 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/hgTracks/bamTrack.c 1.16 - lines changed: 6, context: html, text, full: html, text
- Display wigFetchMinMaxYWithCart's warning about missing data range settings only when we're on hgwdev.
- src/hg/lib/wiggleCart.c 1.30 - lines changed: 1, 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/hgc/bamClick.c 1.12 - lines changed: 18, 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.
- src/hg/hgTracks/bamTrack.c 1.17 - lines changed: 21, 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/hgTrackUi/hgTrackUi.c 1.508 - lines changed: 5, context: html, text, full: html, text
- src/hg/hgTracks/bamTrack.c 1.18 - lines changed: 46, 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).
- src/hg/lib/bamFile.c 1.16 - lines changed: 28, 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/makeDb/trackDb/human/hg18/trackDb.ra 1.431 - lines changed: 24, context: html, text, full: html, text
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