18f572b767889300089237bcada2073f46cd06f5 markd Wed Feb 8 11:59:16 2017 -0800 added more label options and made more readable diff --git src/hg/lib/bigTransMap.as src/hg/lib/bigTransMap.as index 4fd6e1b..56505c6 100644 --- src/hg/lib/bigTransMap.as +++ src/hg/lib/bigTransMap.as @@ -1,48 +1,49 @@ table bigTransMap "bigPsl derived pairwise alignment with additional information" ( string chrom; "Reference sequence chromosome or scaffold" uint chromStart; "Start position in chromosome" uint chromEnd; "End position in chromosome" - string name; "transcript Id" + string name; "alignment Id" uint score; "Score (0-1000), faction identity * 1000" char[1] strand; "+ or - indicates whether the query aligns to the + or - strand on the reference" uint thickStart; "Start of where display should be thick (start codon)" uint thickEnd; "End of where display should be thick (stop codon)" uint reserved; "RGB value (use R,G,B string in input file)" int blockCount; "Number of blocks" int[blockCount] blockSizes; "Comma separated list of block sizes" int[blockCount] chromStarts; "Start positions relative to chromStart" uint oChromStart;"Start position in other chromosome" uint oChromEnd; "End position in other chromosome" char[1] oStrand; "+ or -, - means that psl was reversed into BED-compatible coordinates" uint oChromSize; "Size of other chromosome." int[blockCount] oChromStarts; "Start positions relative to oChromStart or from oChromStart+oChromSize depending on strand" lstring oSequence; "Sequence on other chrom (or edit list, or empty)" lstring oCDS; "CDS in NCBI format" uint chromSize;"Size of target chromosome" uint match; "Number of bases matched." uint misMatch; " Number of bases that don't match " uint repMatch; " Number of bases that match but are part of repeats " uint nCount; " Number of 'N' bases " uint seqType; "0=empty, 1=nucleotide, 2=amino_acid" - string srcDb; "source organism database names" - string srcChrom; "source organism chromosome name" + string srcDb; "source database" + string srcTransId; "source transcript id" + string srcChrom; "source chromosome" uint srcChromStart; "start position in source chromosome" uint srcChromEnd; "end position in source chromosome" uint srcScore; "source source (faction identity * 1000) uint srcAligned; "fraction of source aligned (faction identity * 1000) string geneName; "gene name" string geneId; "gene id" string geneType; "gene type" string transcriptType; "transcript type" string chainType; "type of chains used for mapping" string commonName; "common name" string scientificName; "scientific name" string orgAbbrev; "organism abbreviation" )