File Changes for angie

v265_base to v266_preview (2012-03-27 to 2012-04-10) v266

• src/hg/inc/annoGrateWig.h
  • lines changed 11, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamWig and annoGrateWig,which led to some significant changes: annoRow is now polymorphic (words[] vs. wig float[]), annoFilter has a new function to apply filter(s) to a single number, and annoFormatTab can print out per-base wiggle values or average wiggle values (hardcoded to do per-base until a real config option is added). One puny test case was verified against mysql & table browser output.
• src/hg/inc/annoStreamDb.h
  • lines changed 5, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): instead of having a callercreate the sql connection outside of annoStreamDb, and have to remember not to share it, just allocate the connection inside annoStreamDb. This introduces a dependency on hdb, but I guess that's inevitable. :)
• src/hg/inc/annoStreamWig.h
  • lines changed 11, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamWig and annoGrateWig,which led to some significant changes: annoRow is now polymorphic (words[] vs. wig float[]), annoFilter has a new function to apply filter(s) to a single number, and annoFormatTab can print out per-base wiggle values or average wiggle values (hardcoded to do per-base until a real config option is added). One puny test case was verified against mysql & table browser output.
• src/hg/inc/wiggle.h
  • lines changed 19, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamWig and annoGrateWig,which led to some significant changes: annoRow is now polymorphic (words[] vs. wig float[]), annoFilter has a new function to apply filter(s) to a single number, and annoFormatTab can print out per-base wiggle values or average wiggle values (hardcoded to do per-base until a real config option is added). One puny test case was verified against mysql & table browser output.
• src/hg/lib/annoGrateWig.c
  • lines changed 78, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamWig and annoGrateWig,which led to some significant changes: annoRow is now polymorphic (words[] vs. wig float[]), annoFilter has a new function to apply filter(s) to a single number, and annoFormatTab can print out per-base wiggle values or average wiggle values (hardcoded to do per-base until a real config option is added). One puny test case was verified against mysql & table browser output.
  • lines changed 1, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
• src/hg/lib/annoStreamDb.c
  • lines changed 14, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): instead of having a callercreate the sql connection outside of annoStreamDb, and have to remember not to share it, just allocate the connection inside annoStreamDb. This introduces a dependency on hdb, but I guess that's inevitable. :)
  • lines changed 3, context: html, text, full: html, text
    bugfix for #6152: was skipping the bin column twice, oops.
  • lines changed 1, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
• src/hg/lib/annoStreamWig.c
  • lines changed 152, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamWig and annoGrateWig,which led to some significant changes: annoRow is now polymorphic (words[] vs. wig float[]), annoFilter has a new function to apply filter(s) to a single number, and annoFormatTab can print out per-base wiggle values or average wiggle values (hardcoded to do per-base until a real config option is added). One puny test case was verified against mysql & table browser output.
  • lines changed 3, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamWig and annoGrateWig,which led to some significant changes: annoRow is now polymorphic (words[] vs. wig float[]), annoFilter has a new function to apply filter(s) to a single number, and annoFormatTab can print out per-base wiggle values or average wiggle values (hardcoded to do per-base until a real config option is added). One puny test case was verified against mysql & table browser output.
• src/hg/lib/tests/annoGratorTester.c
  • lines changed 9, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): instead of having a callercreate the sql connection outside of annoStreamDb, and have to remember not to share it, just allocate the connection inside annoStreamDb. This introduces a dependency on hdb, but I guess that's inevitable. :)
  • lines changed 74, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamWig and annoGrateWig,which led to some significant changes: annoRow is now polymorphic (words[] vs. wig float[]), annoFilter has a new function to apply filter(s) to a single number, and annoFormatTab can print out per-base wiggle values or average wiggle values (hardcoded to do per-base until a real config option is added). One puny test case was verified against mysql & table browser output.
  • lines changed 90, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
• src/hg/lib/tests/annoGratorTests.mk
  • lines changed 5, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamWig and annoGrateWig,which led to some significant changes: annoRow is now polymorphic (words[] vs. wig float[]), annoFilter has a new function to apply filter(s) to a single number, and annoFormatTab can print out per-base wiggle values or average wiggle values (hardcoded to do per-base until a real config option is added). One puny test case was verified against mysql & table browser output.
  • lines changed 9, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
• src/hg/lib/tests/expected/annoGrator/snpConsDbToTabOutShort.txt
  • lines changed 39, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamWig and annoGrateWig,which led to some significant changes: annoRow is now polymorphic (words[] vs. wig float[]), annoFilter has a new function to apply filter(s) to a single number, and annoFormatTab can print out per-base wiggle values or average wiggle values (hardcoded to do per-base until a real config option is added). One puny test case was verified against mysql & table browser output.
• src/hg/lib/tests/expected/annoGrator/vcfEx1.txt
  • lines changed 110, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
• src/hg/lib/tests/expected/annoGrator/vcfEx2.txt
  • lines changed 120, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
• src/hg/makeDb/doc/hg18.txt
  • lines changed 4, context: html, text, full: html, text
    Track #1656 (GWAS Catalog): bi-monthly update.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 4, context: html, text, full: html, text
    Track #1656 (GWAS Catalog): bi-monthly update.
• src/inc/annoFilter.h
  • lines changed 5, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamWig and annoGrateWig,which led to some significant changes: annoRow is now polymorphic (words[] vs. wig float[]), annoFilter has a new function to apply filter(s) to a single number, and annoFormatTab can print out per-base wiggle values or average wiggle values (hardcoded to do per-base until a real config option is added). One puny test case was verified against mysql & table browser output.
• src/inc/annoFormatter.h
  • lines changed 14, context: html, text, full: html, text
    Fixing style errors found by Brian in code review: public methodsdefined in structs are functions, so the comment should go below the definition not above.
• src/inc/annoGrator.h
  • lines changed 1, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
  • lines changed 5, context: html, text, full: html, text
    Fixing style errors found by Brian in code review: public methodsdefined in structs are functions, so the comment should go below the definition not above.
• src/inc/annoRow.h
  • lines changed 16, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamWig and annoGrateWig,which led to some significant changes: annoRow is now polymorphic (words[] vs. wig float[]), annoFilter has a new function to apply filter(s) to a single number, and annoFormatTab can print out per-base wiggle values or average wiggle values (hardcoded to do per-base until a real config option is added). One puny test case was verified against mysql & table browser output.
  • lines changed 8, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
• src/inc/annoStreamVcf.h
  • lines changed 12, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
• src/inc/annoStreamer.h
  • lines changed 1, context: html, text, full: html, text
    Comment tweak.
  • lines changed 4, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
  • lines changed 17, context: html, text, full: html, text
    Fixing style errors found by Brian in code review: public methodsdefined in structs are functions, so the comment should go below the definition not above.
• src/inc/vcf.h
  • lines changed 17, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
• src/lib/annoFilter.c
  • lines changed 29, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamWig and annoGrateWig,which led to some significant changes: annoRow is now polymorphic (words[] vs. wig float[]), annoFilter has a new function to apply filter(s) to a single number, and annoFormatTab can print out per-base wiggle values or average wiggle values (hardcoded to do per-base until a real config option is added). One puny test case was verified against mysql & table browser output.
• src/lib/annoFormatTab.c
  • lines changed 81, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamWig and annoGrateWig,which led to some significant changes: annoRow is now polymorphic (words[] vs. wig float[]), annoFilter has a new function to apply filter(s) to a single number, and annoFormatTab can print out per-base wiggle values or average wiggle values (hardcoded to do per-base until a real config option is added). One puny test case was verified against mysql & table browser output.
  • lines changed 10, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
• src/lib/annoGrator.c
  • lines changed 7, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
• src/lib/annoGratorQuery.c
  • lines changed 1, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamWig and annoGrateWig,which led to some significant changes: annoRow is now polymorphic (words[] vs. wig float[]), annoFilter has a new function to apply filter(s) to a single number, and annoFormatTab can print out per-base wiggle values or average wiggle values (hardcoded to do per-base until a real config option is added). One puny test case was verified against mysql & table browser output.
  • lines changed 3, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
• src/lib/annoRow.c
  • lines changed 57, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamWig and annoGrateWig,which led to some significant changes: annoRow is now polymorphic (words[] vs. wig float[]), annoFilter has a new function to apply filter(s) to a single number, and annoFormatTab can print out per-base wiggle values or average wiggle values (hardcoded to do per-base until a real config option is added). One puny test case was verified against mysql & table browser output.
  • lines changed 16, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
• src/lib/annoStreamVcf.c
  • lines changed 135, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
• src/lib/annoStreamer.c
  • lines changed 1, context: html, text, full: html, text
    Comment tweak.
  • lines changed 1, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
• src/lib/linefile.c
  • lines changed 1, context: html, text, full: html, text
    lineFileTabixMayOpen: initialize lf->tabixIter to ti_iter_first sowe can start reading lines from the beginning of the tabix-indexed file, without having to make an iterator for a specific region.
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
• src/lib/vcf.c
  • lines changed 60, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.