File Changes for angie

v323_preview2 to v323_base (2015-09-28 to 2015-10-05) v323

• src/hg/lib/annoStreamDb.c
  • lines changed 164, context: html, text, full: html, text
    Add test cases (and bug fixes!) to make sure that we get the desired
    behavior when an insertion is adjacent to a non-insertion, and when
    an insertion falls at the start or end of the search region (if applicable):
    
    - Include insertions that fall at the start or end of the search region
    
    - If the primary row is an insertion, keep secondary non-insertion rows
    to the left and right.
    
    - If the primary row is a non-insertion, keep secondary insertion rows
    at its start and end.
    
    (i.e. keep insertions at boundaries -- but don't let any non-insertions
    slip through)
    
    The VCF logic is more complicated because VCF indels always include an
    extra base to the left, so they appear to start before they actually do,
    and can be interspersed with non-indels that start there.
    
• src/hg/lib/bed.sql
  • lines changed 1, context: html, text, full: html, text
    Add test cases (and bug fixes!) to make sure that we get the desired
    behavior when an insertion is adjacent to a non-insertion, and when
    an insertion falls at the start or end of the search region (if applicable):
    
    - Include insertions that fall at the start or end of the search region
    
    - If the primary row is an insertion, keep secondary non-insertion rows
    to the left and right.
    
    - If the primary row is a non-insertion, keep secondary insertion rows
    at its start and end.
    
    (i.e. keep insertions at boundaries -- but don't let any non-insertions
    slip through)
    
    The VCF logic is more complicated because VCF indels always include an
    extra base to the left, so they appear to start before they actually do,
    and can be interspersed with non-indels that start there.
    
• src/hg/lib/hdb.c
  • lines changed 6, context: html, text, full: html, text
    hFindTableInfoWithConn was checking table existence when chrom was given,
    but not when chrom was NULL, and so it failed to check existence for a
    table when looking in hgFixed. Now it always checks existence.
    Also, it uses hTableExists (cached) instead of sqlTableExists.
    refs #16112
    
• src/hg/lib/tests/annoGratorTester.c
  • lines changed 64, context: html, text, full: html, text
    Add test cases (and bug fixes!) to make sure that we get the desired
    behavior when an insertion is adjacent to a non-insertion, and when
    an insertion falls at the start or end of the search region (if applicable):
    
    - Include insertions that fall at the start or end of the search region
    
    - If the primary row is an insertion, keep secondary non-insertion rows
    to the left and right.
    
    - If the primary row is a non-insertion, keep secondary insertion rows
    at its start and end.
    
    (i.e. keep insertions at boundaries -- but don't let any non-insertions
    slip through)
    
    The VCF logic is more complicated because VCF indels always include an
    extra base to the left, so they appear to start before they actually do,
    and can be interspersed with non-indels that start there.
    
  • lines changed 10, context: html, text, full: html, text
    Test & fix VCF+tabix querying of insertion items.
    
• src/hg/lib/tests/annoGratorTests.mk
  • lines changed 15, context: html, text, full: html, text
    Add test cases (and bug fixes!) to make sure that we get the desired
    behavior when an insertion is adjacent to a non-insertion, and when
    an insertion falls at the start or end of the search region (if applicable):
    
    - Include insertions that fall at the start or end of the search region
    
    - If the primary row is an insertion, keep secondary non-insertion rows
    to the left and right.
    
    - If the primary row is a non-insertion, keep secondary insertion rows
    at its start and end.
    
    (i.e. keep insertions at boundaries -- but don't let any non-insertions
    slip through)
    
    The VCF logic is more complicated because VCF indels always include an
    extra base to the left, so they appear to start before they actually do,
    and can be interspersed with non-indels that start there.
    
• src/hg/lib/tests/expected/annoGrator/insertions.txt
  • lines changed 212, context: html, text, full: html, text
    Add test cases (and bug fixes!) to make sure that we get the desired
    behavior when an insertion is adjacent to a non-insertion, and when
    an insertion falls at the start or end of the search region (if applicable):
    
    - Include insertions that fall at the start or end of the search region
    
    - If the primary row is an insertion, keep secondary non-insertion rows
    to the left and right.
    
    - If the primary row is a non-insertion, keep secondary insertion rows
    at its start and end.
    
    (i.e. keep insertions at boundaries -- but don't let any non-insertions
    slip through)
    
    The VCF logic is more complicated because VCF indels always include an
    extra base to the left, so they appear to start before they actually do,
    and can be interspersed with non-indels that start there.
    
  • lines changed 4, context: html, text, full: html, text
    Added another test case: first item in primary is an insertion and first item
    in secondary is adjacent on the left.
    
  • lines changed 96, context: html, text, full: html, text
    Test & fix VCF+tabix querying of insertion items.
    
• src/hg/lib/tests/input/annoGrator/insertionsPrimary.bb
  • lines changed 0, context: html, text, full: html, text
    Add test cases (and bug fixes!) to make sure that we get the desired
    behavior when an insertion is adjacent to a non-insertion, and when
    an insertion falls at the start or end of the search region (if applicable):
    
    - Include insertions that fall at the start or end of the search region
    
    - If the primary row is an insertion, keep secondary non-insertion rows
    to the left and right.
    
    - If the primary row is a non-insertion, keep secondary insertion rows
    at its start and end.
    
    (i.e. keep insertions at boundaries -- but don't let any non-insertions
    slip through)
    
    The VCF logic is more complicated because VCF indels always include an
    extra base to the left, so they appear to start before they actually do,
    and can be interspersed with non-indels that start there.
    
  • lines changed 0, context: html, text, full: html, text
    Added another test case: first item in primary is an insertion and first item
    in secondary is adjacent on the left.
    
• src/hg/lib/tests/input/annoGrator/insertionsPrimary.bed
  • lines changed 16, context: html, text, full: html, text
    Add test cases (and bug fixes!) to make sure that we get the desired
    behavior when an insertion is adjacent to a non-insertion, and when
    an insertion falls at the start or end of the search region (if applicable):
    
    - Include insertions that fall at the start or end of the search region
    
    - If the primary row is an insertion, keep secondary non-insertion rows
    to the left and right.
    
    - If the primary row is a non-insertion, keep secondary insertion rows
    at its start and end.
    
    (i.e. keep insertions at boundaries -- but don't let any non-insertions
    slip through)
    
    The VCF logic is more complicated because VCF indels always include an
    extra base to the left, so they appear to start before they actually do,
    and can be interspersed with non-indels that start there.
    
  • lines changed 2, context: html, text, full: html, text
    Added another test case: first item in primary is an insertion and first item
    in secondary is adjacent on the left.
    
• src/hg/lib/tests/input/annoGrator/insertionsPrimary.vcf
  • lines changed 18, context: html, text, full: html, text
    Add test cases (and bug fixes!) to make sure that we get the desired
    behavior when an insertion is adjacent to a non-insertion, and when
    an insertion falls at the start or end of the search region (if applicable):
    
    - Include insertions that fall at the start or end of the search region
    
    - If the primary row is an insertion, keep secondary non-insertion rows
    to the left and right.
    
    - If the primary row is a non-insertion, keep secondary insertion rows
    at its start and end.
    
    (i.e. keep insertions at boundaries -- but don't let any non-insertions
    slip through)
    
    The VCF logic is more complicated because VCF indels always include an
    extra base to the left, so they appear to start before they actually do,
    and can be interspersed with non-indels that start there.
    
  • lines changed 9, context: html, text, full: html, text
    Added another test case: first item in primary is an insertion and first item
    in secondary is adjacent on the left.
    
• src/hg/lib/tests/input/annoGrator/insertionsPrimary.vcf.gz
  • lines changed 0, context: html, text, full: html, text
    Test & fix VCF+tabix querying of insertion items.
    
• src/hg/lib/tests/input/annoGrator/insertionsPrimary.vcf.gz.tbi
  • lines changed 0, context: html, text, full: html, text
    Test & fix VCF+tabix querying of insertion items.
    
• src/hg/lib/tests/input/annoGrator/insertionsSecondary.bb
  • lines changed 0, context: html, text, full: html, text
    Add test cases (and bug fixes!) to make sure that we get the desired
    behavior when an insertion is adjacent to a non-insertion, and when
    an insertion falls at the start or end of the search region (if applicable):
    
    - Include insertions that fall at the start or end of the search region
    
    - If the primary row is an insertion, keep secondary non-insertion rows
    to the left and right.
    
    - If the primary row is a non-insertion, keep secondary insertion rows
    at its start and end.
    
    (i.e. keep insertions at boundaries -- but don't let any non-insertions
    slip through)
    
    The VCF logic is more complicated because VCF indels always include an
    extra base to the left, so they appear to start before they actually do,
    and can be interspersed with non-indels that start there.
    
  • lines changed 0, context: html, text, full: html, text
    Added another test case: first item in primary is an insertion and first item
    in secondary is adjacent on the left.
    
• src/hg/lib/tests/input/annoGrator/insertionsSecondary.bed
  • lines changed 25, context: html, text, full: html, text
    Add test cases (and bug fixes!) to make sure that we get the desired
    behavior when an insertion is adjacent to a non-insertion, and when
    an insertion falls at the start or end of the search region (if applicable):
    
    - Include insertions that fall at the start or end of the search region
    
    - If the primary row is an insertion, keep secondary non-insertion rows
    to the left and right.
    
    - If the primary row is a non-insertion, keep secondary insertion rows
    at its start and end.
    
    (i.e. keep insertions at boundaries -- but don't let any non-insertions
    slip through)
    
    The VCF logic is more complicated because VCF indels always include an
    extra base to the left, so they appear to start before they actually do,
    and can be interspersed with non-indels that start there.
    
  • lines changed 2, context: html, text, full: html, text
    Added another test case: first item in primary is an insertion and first item
    in secondary is adjacent on the left.
    
• src/hg/lib/tests/input/annoGrator/insertionsSecondary.vcf
  • lines changed 43, context: html, text, full: html, text
    Add test cases (and bug fixes!) to make sure that we get the desired
    behavior when an insertion is adjacent to a non-insertion, and when
    an insertion falls at the start or end of the search region (if applicable):
    
    - Include insertions that fall at the start or end of the search region
    
    - If the primary row is an insertion, keep secondary non-insertion rows
    to the left and right.
    
    - If the primary row is a non-insertion, keep secondary insertion rows
    at its start and end.
    
    (i.e. keep insertions at boundaries -- but don't let any non-insertions
    slip through)
    
    The VCF logic is more complicated because VCF indels always include an
    extra base to the left, so they appear to start before they actually do,
    and can be interspersed with non-indels that start there.
    
  • lines changed 5, context: html, text, full: html, text
    Added another test case: first item in primary is an insertion and first item
    in secondary is adjacent on the left.
    
  • lines changed 0, context: html, text, full: html, text
    Test & fix VCF+tabix querying of insertion items.
    
• src/hg/lib/tests/input/annoGrator/insertionsSecondary.vcf.gz
  • lines changed 0, context: html, text, full: html, text
    Test & fix VCF+tabix querying of insertion items.
    
• src/hg/lib/tests/input/annoGrator/insertionsSecondary.vcf.gz.tbi
  • lines changed 0, context: html, text, full: html, text
    Test & fix VCF+tabix querying of insertion items.
    
• src/lib/annoFormatTab.c
  • lines changed 72, context: html, text, full: html, text
    On very long queries like selected fields of snp144 chr1 (>11M rows),
    hgIntegrator was spending about half of the time repetitively building
    up sourceName.columnName strings and looking them up in a hash to tell
    whether or not to include each column's data in the output. To avoid
    the waste, now it builds up an array (one for each source, primary +
    grators) of arrays of flags (one flag for each column) so it can do
    an array lookup instead of string-munging and hash lookup.
    ~2x speedup for selected fields of snp144 chr1 (4 minutes -> 2 minutes).
    mysql time is about half that; much of the other half is copying data
    in annoStreamDb.c:bufferRowsFromSqlQuery.
    
• src/lib/annoGrator.c
  • lines changed 49, context: html, text, full: html, text
    Add test cases (and bug fixes!) to make sure that we get the desired
    behavior when an insertion is adjacent to a non-insertion, and when
    an insertion falls at the start or end of the search region (if applicable):
    
    - Include insertions that fall at the start or end of the search region
    
    - If the primary row is an insertion, keep secondary non-insertion rows
    to the left and right.
    
    - If the primary row is a non-insertion, keep secondary insertion rows
    at its start and end.
    
    (i.e. keep insertions at boundaries -- but don't let any non-insertions
    slip through)
    
    The VCF logic is more complicated because VCF indels always include an
    extra base to the left, so they appear to start before they actually do,
    and can be interspersed with non-indels that start there.
    
• src/lib/annoStreamTab.c
  • lines changed 36, context: html, text, full: html, text
    Add test cases (and bug fixes!) to make sure that we get the desired
    behavior when an insertion is adjacent to a non-insertion, and when
    an insertion falls at the start or end of the search region (if applicable):
    
    - Include insertions that fall at the start or end of the search region
    
    - If the primary row is an insertion, keep secondary non-insertion rows
    to the left and right.
    
    - If the primary row is a non-insertion, keep secondary insertion rows
    at its start and end.
    
    (i.e. keep insertions at boundaries -- but don't let any non-insertions
    slip through)
    
    The VCF logic is more complicated because VCF indels always include an
    extra base to the left, so they appear to start before they actually do,
    and can be interspersed with non-indels that start there.
    
• src/lib/annoStreamVcf.c
  • lines changed 24, context: html, text, full: html, text
    Add test cases (and bug fixes!) to make sure that we get the desired
    behavior when an insertion is adjacent to a non-insertion, and when
    an insertion falls at the start or end of the search region (if applicable):
    
    - Include insertions that fall at the start or end of the search region
    
    - If the primary row is an insertion, keep secondary non-insertion rows
    to the left and right.
    
    - If the primary row is a non-insertion, keep secondary insertion rows
    at its start and end.
    
    (i.e. keep insertions at boundaries -- but don't let any non-insertions
    slip through)
    
    The VCF logic is more complicated because VCF indels always include an
    extra base to the left, so they appear to start before they actually do,
    and can be interspersed with non-indels that start there.
    
  • lines changed 4, context: html, text, full: html, text
    Test & fix VCF+tabix querying of insertion items.
    
• src/lib/bigBed.c
  • lines changed 9, context: html, text, full: html, text
    Add test cases (and bug fixes!) to make sure that we get the desired
    behavior when an insertion is adjacent to a non-insertion, and when
    an insertion falls at the start or end of the search region (if applicable):
    
    - Include insertions that fall at the start or end of the search region
    
    - If the primary row is an insertion, keep secondary non-insertion rows
    to the left and right.
    
    - If the primary row is a non-insertion, keep secondary insertion rows
    at its start and end.
    
    (i.e. keep insertions at boundaries -- but don't let any non-insertions
    slip through)
    
    The VCF logic is more complicated because VCF indels always include an
    extra base to the left, so they appear to start before they actually do,
    and can be interspersed with non-indels that start there.