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comparison bigPsl.as @ 6:237707a6b74d draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
author yating-l
date Thu, 15 Feb 2018 17:05:05 -0500
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5:e762f4b9e4bd 6:237707a6b74d
1 table bigPsl
2 "bigPsl pairwise alignment"
3 (
4 string chrom; "Reference sequence chromosome or scaffold"
5 uint chromStart; "Start position in chromosome"
6 uint chromEnd; "End position in chromosome"
7 string name; "Name or ID of item, ideally both human readable and unique"
8 uint score; "Score (0-1000)"
9 char[1] strand; "+ or - for strand"
10 uint thickStart; "Start of where display should be thick (start codon)"
11 uint thickEnd; "End of where display should be thick (stop codon)"
12 uint reserved; "RGB value (use R,G,B string in input file)"
13 int blockCount; "Number of blocks"
14 int[blockCount] blockSizes; "Comma separated list of block sizes"
15 int[blockCount] chromStarts; "Start positions relative to chromStart"
16
17 uint oChromStart;"Start position in other chromosome"
18 uint oChromEnd; "End position in other chromosome"
19 char[1] oStrand; "+ or - for other strand"
20 uint oChromSize; "Size of other chromosome."
21 int[blockCount] oChromStarts; "Start positions relative to oChromStart"
22
23 lstring oSequence; "Sequence on other chrom (or edit list, or empty)"
24 string oCDS; "CDS in NCBI format"
25
26 uint chromSize;"Size of target chromosome"
27
28 uint match; "Number of bases matched."
29 uint misMatch; " Number of bases that don't match "
30 uint repMatch; " Number of bases that match but are part of repeats "
31 uint nCount; " Number of 'N' bases "
32 )
33