Mercurial > repos > yating-l > hubarchivecreator
comparison bigPsl.as @ 0:f493979f1408 draft default tip
planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
| author | yating-l |
|---|---|
| date | Wed, 21 Dec 2016 12:13:04 -0500 |
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| children |
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| -1:000000000000 | 0:f493979f1408 |
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| 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 |