A small program for interpolating genetic map distances
C++
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src initial version Dec 22, 2013
LICENSE.md initial version Dec 22, 2013
README initial version Dec 22, 2013
test.map initial version Dec 22, 2013
test.query initial version Dec 22, 2013

README

To compile, type make in the src/ directory.

To test the program try ./predictGMAP --ref test.map --query test.query --out test.predicted.map

This program is intended to take a reference genetic map and a set of query positions and output genetic map
information at each query position.  If possible, missing query positions will be interpolated based on the 
reference genetic map.  If a query position falls within a large gap in the reference map file, the position 
is skipped.

++++++++++Command Line Arguments++++++++++

--help <bool> Prints this help dialog.
--max-gap <double> If a gap of > MAX_GAP is encountered in the reference map file, do not interpolate in between. Default: 18848.64, dervied from the standard deviation in gap lengths from the HapMap genetic map.
--out <string> The name of the output file. Default: predictGMAP.outfile.map
--query <string> A list of physical positions at which you desire a genetic map.
--ref <string> The reference genetic map file with format: <chr#> <locusID> <genetic pos> <physical pos>