Basic Usage

rearrangement (--help|-help|-h)
rearrangement <inputFile 3<refFile [options]

inputFile

The one-line format is

query<tab>count<tab>refId<newline>

query is the query sequence. count is the duplicate number of the query. refId indicates the 0-based line number of reference in refFline

refFile

The one-line format is

s1<tab>ref1<tab>e1<tab>s2<tab>ref2<tab>e2<tab>...<tab>sN<tab>refN<tab>eN<newline>

sM and eM are the central range of ref1. The regions upstream to sM or downstream to eM are extension regions. The match bonus for extension regions are less than those for central region.

outputFile

The three-line format is

index<tab>count<tab>score<tab>refId<newline>
refLine<newline>
queryLine<newline>

index is the 1-based alignment index as 1, 2, 3 and so on. count is copied from inputFile. score is the alignment score. refId is copied from inputFile. refLine and queryLine form the actual alignment.