Commits for angie
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v284_preview to v284_preview2 (2013-05-14 to 2013-05-21) v284
- Added 2 new args to annoStreamer:nextRow: minChrom and minEnd(which could also be called regionStart depending on point of view).
Streamers may use those hints to skip over data that precedes
minChrom and minEnd, to avoid the overhead of creating annoRows
that annoGrators will then have to skip over. When primary data
are sparse and grator data are very dense, this saves significant
memory and user-cycles. Unfortunately mysql can still be the
bottleneck for elapsed time. Room for improvement in annoStreamDb:
when assembly has a reasonably small number of sequences (<1000),
genome-wide queries could be internally broken down into per-seq
queries; that would let us skip over chroms that precede minChrom.
refs #6152
- src/hg/lib/annoStreamDb.c - lines changed 29, context: html, text, full: html, text
- src/hg/lib/annoStreamWig.c - lines changed 3, context: html, text, full: html, text
- src/lib/annoGratorQuery.c - lines changed 1, context: html, text, full: html, text
- src/lib/annoStreamBigBed.c - lines changed 23, context: html, text, full: html, text
- src/lib/annoStreamBigWig.c - lines changed 25, context: html, text, full: html, text
- src/lib/annoStreamTab.c - lines changed 31, context: html, text, full: html, text
- src/lib/annoStreamVcf.c - lines changed 49, context: html, text, full: html, text
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