File Changes for angie

v282_preview2 to v282_base (2013-04-09 to 2013-04-16) v282

• src/hg/lib/annoGratorGpVar.c
  • lines changed 64, context: html, text, full: html, text
    Use localmem for annoRow storage, instead of many independent malloc & free calls. refs #6152
• src/hg/lib/annoStreamDb.c
  • lines changed 40, context: html, text, full: html, text
    Use localmem for annoRow storage, instead of many independent malloc & free calls. refs #6152
  • lines changed 31, context: html, text, full: html, text
    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/annoStreamWig.c
  • lines changed 5, context: html, text, full: html, text
    Use localmem for annoRow storage, instead of many independent malloc & free calls. refs #6152
• src/hg/lib/tests/annoGratorTester.c
  • lines changed 24, context: html, text, full: html, text
    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/tests/annoGratorTests.mk
  • lines changed 1, context: html, text, full: html, text
    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/inc/annoGrator.h
  • lines changed 4, context: html, text, full: html, text
    Use localmem for annoRow storage, instead of many independent malloc & free calls. refs #6152
• src/inc/annoRow.h
  • lines changed 15, context: html, text, full: html, text
    Use localmem for annoRow storage, instead of many independent malloc & free calls. refs #6152
• src/inc/annoStreamTab.h
  • lines changed 12, context: html, text, full: html, text
    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/inc/annoStreamer.h
  • lines changed 1, context: html, text, full: html, text
    Use localmem for annoRow storage, instead of many independent malloc & free calls. refs #6152
  • lines changed 8, context: html, text, full: html, text
    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/lib/annoGrateWig.c
  • lines changed 34, context: html, text, full: html, text
    Use localmem for annoRow storage, instead of many independent malloc & free calls. refs #6152
• src/lib/annoGrator.c
  • lines changed 26, context: html, text, full: html, text
    Use localmem for annoRow storage, instead of many independent malloc & free calls. refs #6152
• src/lib/annoGratorQuery.c
  • lines changed 9, context: html, text, full: html, text
    Use localmem for annoRow storage, instead of many independent malloc & free calls. refs #6152
• src/lib/annoRow.c
  • lines changed 72, context: html, text, full: html, text
    Use localmem for annoRow storage, instead of many independent malloc & free calls. refs #6152
• src/lib/annoStreamBigBed.c
  • lines changed 3, context: html, text, full: html, text
    Use localmem for annoRow storage, instead of many independent malloc & free calls. refs #6152
• src/lib/annoStreamBigWig.c
  • lines changed 5, context: html, text, full: html, text
    Use localmem for annoRow storage, instead of many independent malloc & free calls. refs #6152
• src/lib/annoStreamTab.c
  • lines changed 214, context: html, text, full: html, text
    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/lib/annoStreamVcf.c
  • lines changed 2, context: html, text, full: html, text
    Use localmem for annoRow storage, instead of many independent malloc & free calls. refs #6152
• src/lib/annoStreamer.c
  • lines changed 43, context: html, text, full: html, text
    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/lib/bamFile.c
  • lines changed 2, context: html, text, full: html, text
    Fixing strict-gcc warning "‘return’ with a value, in function returning void"
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    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.