sim4db tools as of July 17, 2006

filterPolishes
headPolishes
mappedCoverage
mergePolishes
sortPolishes
pickBestPolish
pickUniquePolish
pickUniquePolish-nhgri
cleanPolishes
fixPolishesIID
plotIntronSize
plotCoverageVsIdentity
parseSNP
comparePolishes
convertToAtac
trimSequencesBasedOnMatches
uniqPolishes
summarizePolishes
removeDuplicate
vennPolishes
realignPolishes
removeRedundant
reportAlignmentDifferences

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filterPolishes

Filters polishes by percent identity, percent coverage, length of
alignment (number of matches), number of exons, query of genomic IID.
Can segregate polishes, placing polishes for each genomic IID into a
separate file.

Also, can remove deflines or alignments, and can "normalize" the
genomic coordinates by adding in the match offset.

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headPolishes

Like the UNIX head command, returns the first N polishes in a file.

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mappedCoverage

Returns the percentage of each query that is covered by an alignment.
Also can mask out those regions with N's.

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mergePolishes

Merges multiple sets of polishes, mapped to the same genomic
sequences, into one file, updating the query IID.

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sortPolishes



pickBestPolish
pickUniquePolish
pickUniquePolish-nhgri
cleanPolishes
fixPolishesIID
plotIntronSize
plotCoverageVsIdentity
parseSNP
comparePolishes
convertToAtac
trimSequencesBasedOnMatches
uniqPolishes
summarizePolishes
removeDuplicate
vennPolishes
realignPolishes
removeRedundant
reportAlignmentDifferences
