Export functions for UCSC genome BLAT alignments

Description Usage Arguments Value Author(s)

Take an alignment of targets to chromosome(s) where the minimum requirements are the query name, target name (ie chromosome), start, stop and strand of the alignment.

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  alignment2psl(query = x[, "query"], target = x[, "chr"],
    start = x[, "start"], stop = x[, "stop"],
    strand = x[, "strand"], score = NULL, x)

`query`	a character vector of query names
`target`	a vector of chromosome numbers; either chr1, chrX or 1, "X" etc...
`start`	numerical vectors of start of the alignment
`stop`	numerical vectors of stop of the alignment
`strand`	"+" or "-" for each alignment
`score`	alignment score. default=`NULL`
`x`	the alignment object