File Changes for angie

v375_preview2 to v375_base (2018-12-03 to 2018-12-10) v375

• .gitignore
  • lines changed 1, context: html, text, full: html, text
    7fb9856107ffbc3bed974e893a58f299b138cbac Mon Dec 10 09:02:00 2018 -0800
    Ignore gcov-generated .gcno files.
• src/hg/lib/variantProjector.c
  • lines changed 168, context: html, text, full: html, text
    2dd2b7b66f28d7ea799ec463ca1c92e67387ca2d Fri Dec 7 17:04:33 2018 -0800
    Make vpExpandIndelGaps detect and compensate for spurious alignment gaps (no RM; example reported to Terence Murphy at NCBI). This is related to d22f2f9 (galGal6 NM_001030566.1 NCBI alignment introduced unnecessary gaps into a run of 15 A's that should have aligned perfectly). Now we can detect unnecessary gaps that cancel each other out, and restore the larger block that should not have been broken up. We can also delete garbage exons that are eclipsed by an intron's region of ambiguous placement/shifting, absorbing them into the resulting double-sided gap.
• src/hg/oneShot/pslExpandIndelGaps/makefile
  • lines changed 3, context: html, text, full: html, text
    2dd2b7b66f28d7ea799ec463ca1c92e67387ca2d Fri Dec 7 17:04:33 2018 -0800
    Make vpExpandIndelGaps detect and compensate for spurious alignment gaps (no RM; example reported to Terence Murphy at NCBI). This is related to d22f2f9 (galGal6 NM_001030566.1 NCBI alignment introduced unnecessary gaps into a run of 15 A's that should have aligned perfectly). Now we can detect unnecessary gaps that cancel each other out, and restore the larger block that should not have been broken up. We can also delete garbage exons that are eclipsed by an intron's region of ambiguous placement/shifting, absorbing them into the resulting double-sided gap.
• src/hg/oneShot/pslExpandIndelGaps/pslExpandIndelGaps.c
  • lines changed 122, context: html, text, full: html, text
    2dd2b7b66f28d7ea799ec463ca1c92e67387ca2d Fri Dec 7 17:04:33 2018 -0800
    Make vpExpandIndelGaps detect and compensate for spurious alignment gaps (no RM; example reported to Terence Murphy at NCBI). This is related to d22f2f9 (galGal6 NM_001030566.1 NCBI alignment introduced unnecessary gaps into a run of 15 A's that should have aligned perfectly). Now we can detect unnecessary gaps that cancel each other out, and restore the larger block that should not have been broken up. We can also delete garbage exons that are eclipsed by an intron's region of ambiguous placement/shifting, absorbing them into the resulting double-sided gap.
• src/hg/oneShot/pslExpandIndelGaps/tests/expected/ncbiBogusGapsNM.psl
  • lines changed 7, context: html, text, full: html, text
    2dd2b7b66f28d7ea799ec463ca1c92e67387ca2d Fri Dec 7 17:04:33 2018 -0800
    Make vpExpandIndelGaps detect and compensate for spurious alignment gaps (no RM; example reported to Terence Murphy at NCBI). This is related to d22f2f9 (galGal6 NM_001030566.1 NCBI alignment introduced unnecessary gaps into a run of 15 A's that should have aligned perfectly). Now we can detect unnecessary gaps that cancel each other out, and restore the larger block that should not have been broken up. We can also delete garbage exons that are eclipsed by an intron's region of ambiguous placement/shifting, absorbing them into the resulting double-sided gap.
• src/hg/oneShot/pslExpandIndelGaps/tests/expected/ncbiBogusGapsNM.stderr
  • lines changed 14, context: html, text, full: html, text
    2dd2b7b66f28d7ea799ec463ca1c92e67387ca2d Fri Dec 7 17:04:33 2018 -0800
    Make vpExpandIndelGaps detect and compensate for spurious alignment gaps (no RM; example reported to Terence Murphy at NCBI). This is related to d22f2f9 (galGal6 NM_001030566.1 NCBI alignment introduced unnecessary gaps into a run of 15 A's that should have aligned perfectly). Now we can detect unnecessary gaps that cancel each other out, and restore the larger block that should not have been broken up. We can also delete garbage exons that are eclipsed by an intron's region of ambiguous placement/shifting, absorbing them into the resulting double-sided gap.
• src/hg/oneShot/pslExpandIndelGaps/tests/expected/ncbiBogusGapsXM.psl
  • lines changed 1, context: html, text, full: html, text
    2dd2b7b66f28d7ea799ec463ca1c92e67387ca2d Fri Dec 7 17:04:33 2018 -0800
    Make vpExpandIndelGaps detect and compensate for spurious alignment gaps (no RM; example reported to Terence Murphy at NCBI). This is related to d22f2f9 (galGal6 NM_001030566.1 NCBI alignment introduced unnecessary gaps into a run of 15 A's that should have aligned perfectly). Now we can detect unnecessary gaps that cancel each other out, and restore the larger block that should not have been broken up. We can also delete garbage exons that are eclipsed by an intron's region of ambiguous placement/shifting, absorbing them into the resulting double-sided gap.
• src/hg/oneShot/pslExpandIndelGaps/tests/expected/ncbiBogusGapsXM.stderr
  • lines changed 1, context: html, text, full: html, text
    2dd2b7b66f28d7ea799ec463ca1c92e67387ca2d Fri Dec 7 17:04:33 2018 -0800
    Make vpExpandIndelGaps detect and compensate for spurious alignment gaps (no RM; example reported to Terence Murphy at NCBI). This is related to d22f2f9 (galGal6 NM_001030566.1 NCBI alignment introduced unnecessary gaps into a run of 15 A's that should have aligned perfectly). Now we can detect unnecessary gaps that cancel each other out, and restore the larger block that should not have been broken up. We can also delete garbage exons that are eclipsed by an intron's region of ambiguous placement/shifting, absorbing them into the resulting double-sided gap.
• src/hg/oneShot/pslExpandIndelGaps/tests/input/galGal6.NM_001030566.1.psl
  • lines changed 15, context: html, text, full: html, text
    2dd2b7b66f28d7ea799ec463ca1c92e67387ca2d Fri Dec 7 17:04:33 2018 -0800
    Make vpExpandIndelGaps detect and compensate for spurious alignment gaps (no RM; example reported to Terence Murphy at NCBI). This is related to d22f2f9 (galGal6 NM_001030566.1 NCBI alignment introduced unnecessary gaps into a run of 15 A's that should have aligned perfectly). Now we can detect unnecessary gaps that cancel each other out, and restore the larger block that should not have been broken up. We can also delete garbage exons that are eclipsed by an intron's region of ambiguous placement/shifting, absorbing them into the resulting double-sided gap.
• src/hg/oneShot/pslExpandIndelGaps/tests/input/galGal6.XM_025152810.1.psl
  • lines changed 3, context: html, text, full: html, text
    2dd2b7b66f28d7ea799ec463ca1c92e67387ca2d Fri Dec 7 17:04:33 2018 -0800
    Make vpExpandIndelGaps detect and compensate for spurious alignment gaps (no RM; example reported to Terence Murphy at NCBI). This is related to d22f2f9 (galGal6 NM_001030566.1 NCBI alignment introduced unnecessary gaps into a run of 15 A's that should have aligned perfectly). Now we can detect unnecessary gaps that cancel each other out, and restore the larger block that should not have been broken up. We can also delete garbage exons that are eclipsed by an intron's region of ambiguous placement/shifting, absorbing them into the resulting double-sided gap.
• src/hg/oneShot/pslExpandIndelGaps/tests/makefile
  • lines changed 23, context: html, text, full: html, text
    2dd2b7b66f28d7ea799ec463ca1c92e67387ca2d Fri Dec 7 17:04:33 2018 -0800
    Make vpExpandIndelGaps detect and compensate for spurious alignment gaps (no RM; example reported to Terence Murphy at NCBI). This is related to d22f2f9 (galGal6 NM_001030566.1 NCBI alignment introduced unnecessary gaps into a run of 15 A's that should have aligned perfectly). Now we can detect unnecessary gaps that cancel each other out, and restore the larger block that should not have been broken up. We can also delete garbage exons that are eclipsed by an intron's region of ambiguous placement/shifting, absorbing them into the resulting double-sided gap.
• src/hg/utils/pslMismatchGapToBed/pslMismatchGapToBed.c
  • lines changed 6, context: html, text, full: html, text
    d22f2f9bbd1ebebfc1a5d084f4d91700875349dd Wed Dec 5 12:04:31 2018 -0800
    Changing errAbort to warning for unnecessary alignment gaps (reported to Terence Murphy at NCBI) for chicken transcript NM_001030566.1. It's not really a problem for reporting differences, but variantProjector will need a little work in order to handle it.
• src/inc/psl.h
  • lines changed 4, context: html, text, full: html, text
    1791b48abfff1cb403041e39962c4021d3680664 Fri Dec 7 17:03:41 2018 -0800
    Making pslRecalcBounds public for use elsewhere.
• src/lib/psl.c
  • lines changed 1, context: html, text, full: html, text
    1791b48abfff1cb403041e39962c4021d3680664 Fri Dec 7 17:03:41 2018 -0800
    Making pslRecalcBounds public for use elsewhere.