Commits for angie
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v282_preview2 to v282_base (2013-04-09 to 2013-04-16) v282
- Use localmem for annoRow storage, instead of many independent malloc & free calls. refs #6152
- src/hg/lib/annoGratorGpVar.c - lines changed 64, context: html, text, full: html, text
- src/hg/lib/annoStreamDb.c - lines changed 40, context: html, text, full: html, text
- src/hg/lib/annoStreamWig.c - lines changed 5, context: html, text, full: html, text
- src/lib/annoGrateWig.c - lines changed 34, context: html, text, full: html, text
- src/lib/annoGratorQuery.c - lines changed 9, context: html, text, full: html, text
- src/lib/annoStreamBigBed.c - lines changed 3, context: html, text, full: html, text
- src/lib/annoStreamBigWig.c - lines changed 5, context: html, text, full: html, text
- src/lib/annoStreamVcf.c - lines changed 2, context: html, text, full: html, text
- Merge branch 'annoRowLm'
- Fixing strict-gcc warning "‘return’ with a value, in function returning void"
- Adding annoStreamTab and simple test case.refs #6152
Performance will not be good for a series of queries to small regions
on the same chromosome, because even if the regions don't overlap, we
will have to reopen the file every time and start over just in case
there are some items that start to the left of the region but overlap
it.
To fix that, we could add a queue for use when the region is smaller
than a chromosome. Items that end to the right of the region would be
kept in a queue in case they're needed in the next region query. When
a new sub-chrom region query begins, if there are items in the queue
that overlap the new region, they are used first and then we start
reading from the file where we left off at the end of the last region.
- src/hg/lib/annoStreamDb.c - lines changed 31, context: html, text, full: html, text
- src/hg/lib/tests/annoGratorTester.c - lines changed 24, context: html, text, full: html, text
- src/hg/lib/tests/annoGratorTests.mk - lines changed 1, context: html, text, full: html, text
- src/inc/annoStreamTab.h - lines changed 12, context: html, text, full: html, text
- src/lib/annoStreamTab.c - lines changed 214, context: html, text, full: html, text
- src/lib/annoStreamer.c - lines changed 43, context: html, text, full: html, text
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