File Changes for angie

v355_preview to v355_preview2 (2017-09-04 to 2017-09-11) v355

• src/hg/hgc/hgc.c
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    c84bb93c44e2b071ff91f655a89ed866a36cb31c Thu Aug 31 05:17:05 2017 -0700
    Clarify messages displayed when we can't find an alignment in ncbiRefSeqPsl and/or seqNcbiRefSeq.
• src/hg/inc/ncbiRefSeqOther.as
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    ac99b14fc67a6843f6751148bd97358b1f93fddd Sat Sep 9 12:06:12 2017 -0700
    New script to build ncbiRefSeqOther BED with extra columns sourced from an attributes file generated by gff3ToGenePred -attrsOut. Refining attributes for ncbiRefSeqOther: * Split Dbxref into separate columns GeneID, MIM, HGNC, miRBase for linking out * Remove Name2 column which is now redundant with gene column * Remove ncrna_class column which doesn't appear in p11 GFF * Reorder columns to flow a bit better * Reword some column descriptions that appear in hgc table display
• src/hg/makeDb/doc/hg38/ncbiRefSeq.txt
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    fb8c3a6bc30ab45bd090d04b93e8d12e434b90f7 Sat Sep 9 13:31:59 2017 -0700
    Ran updated ncbiRefSeq pipeline on hg38 (NCBI annotation release GCF_000001405.37_GRCh38.p11)
• src/hg/makeDb/trackDb/refSeqComposite.ra
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    a3b4dc2a065b0d8cb6b86142e3d9aaf05524c2cc Wed Aug 30 10:02:50 2017 -0700
    Use gene as the label field for ncbiRefSeqOther.
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    0a601e8e0818ed1b7dcfb3186b21c6d1b112b910 Sat Sep 9 12:07:21 2017 -0700
    Add 'urls' setting to ncbiRefSeqOther to link out to Entrez Gene, OMIM, HGNC and miRBase.
• src/hg/pslRecalcMatch/pslRecalcMatch.c
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    9ab015136bbc854a5dc03b71d5d465771539f6c3 Thu Sep 7 11:31:20 2017 -0700
    pslRecalcMatch: new option -ignoreQMissing for when we have fasta for only a subset of query sequences.
• src/hg/pslSomeRecords/pslSomeRecords.c
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    9ddd5d9026bdcec1b2ff1652c2abc5ddf9f56900 Tue Aug 22 14:35:28 2017 -0700
    pslSomeRecords: fixed interaction of -tToo and -not; support multiple qName+tName combos for -tToo.
• src/hg/utils/automation/doNcbiRefSeq.pl
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    eb3e0997a32a9d1ac61dd848d8bad9217f689e71 Sat Sep 9 12:07:38 2017 -0700
    doNcbiRefSeq.pl: Improvements to ncbiRefSeqPsl and ncbiRefSeqOther generation as well as streamlining some steps. * Check /hive/data/inside $local2Bit independently of /hive/data/outside files so we can still link to outside files if inside files don't exist. * Use gff3ToGenePred -processAllGeneChildren to avoid losing some NR/XR accessions for items with uncommon feature types * Add RefSeq Summary descriptions to ncbiRefSeqLink using gff3ToRefLink.pl (previously the join failed) * Load ncbiRefSeq mysql without ncbiRefSeqOther items * Load ncbiRefSeqOther as bigBed with extra columns not genePred, to be consistent with existing trackDb & released data * Generate trix index for ncbiRefSeqOther * Use both qName and tName in pslSomeRecords so that we don't drop a clean mapping on a regular chrom when the transcript happens to also have an odd mapping on some alt chrom. * Use pslRecalcMatch to get correct misMatches counts in ncbiRefSeqPsl (formerly all 0). * Removed unused bigPsl * Update hgFixed.trackVersion.
• src/hg/utils/automation/gff3ToRefLink.pl
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    b609f36d5cf53941c1444f394814746d1bb93383 Sat Sep 9 12:05:10 2017 -0700
    gff3ToRefLink.pl: get both status and descriptions (RefSeq summaries) from raFile; clean up flattened text within ##*-START / ##*-END semi-structured text sections.
• src/hg/utils/automation/ncbiRefSeqOtherAttrs.pl
  • lines changed 137, context: html, text, full: html, text
    ac99b14fc67a6843f6751148bd97358b1f93fddd Sat Sep 9 12:06:12 2017 -0700
    New script to build ncbiRefSeqOther BED with extra columns sourced from an attributes file generated by gff3ToGenePred -attrsOut. Refining attributes for ncbiRefSeqOther: * Split Dbxref into separate columns GeneID, MIM, HGNC, miRBase for linking out * Remove Name2 column which is now redundant with gene column * Remove ncrna_class column which doesn't appear in p11 GFF * Reorder columns to flow a bit better * Reword some column descriptions that appear in hgc table display
• src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
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    93b0fc1eac4eb20023b87b4933cb94d3c6b5ad8c Thu Aug 24 09:25:38 2017 -0700
    gff3ToGenePred: add option -processAllGeneChildren so we don't have to compare feature type to an ever-expanding list of types used in NCBI GFF3.
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    fd2f56503ce9f077fffdeea36c8602dac0504484 Fri Sep 8 12:08:02 2017 -0700
    gff3ToGenePred: changing some names to be more clear (to me anyway)
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    7505d424eab3a98bef75efab99e4b1312040d337 Fri Sep 8 15:49:27 2017 -0700
    gff3ToGenePred -attrsOut: print attributes for genes in addition to transcripts (for inheritance)
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    9863cd2542194ede314729e866efed9ed7967d0a Fri Sep 8 15:40:18 2017 -0700
    gff3ToGenePred -attrsOut: when attribute value has been split by comma into a list, join the pieces back together instead of printing only the first item.
• src/hg/utils/vcfToHgvs/tests/expected/stopLoss.tab
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    8ee925a2c358c9c7b028bf0a211fb637e3bc099e Sat Sep 9 13:40:30 2017 -0700
    Sort results to prevent test failure caused by different order of transcripts in table.
• src/hg/utils/vcfToHgvs/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    8ee925a2c358c9c7b028bf0a211fb637e3bc099e Sat Sep 9 13:40:30 2017 -0700
    Sort results to prevent test failure caused by different order of transcripts in table.