XPEHH fixed, gzip support

Release of 1.0.3. A critical bug in the XP-EHH module was introduced in version 1.0.2 and has been fixed in 1.0.3. Do not use 1.0.2 for calculating XP-EHH scores. Thanks to David McWilliams for finding this error. 1.0.3 also introduces support for gzipped input files. You may pass hap.gz, map.gz. and tped.gz files interchangably with unzipped files using the same command line arguments. A new command line option is available.

--trunc-ok : If an EHH decay reaches the end of a sequence before reaching the cutoff,
integrate the curve anyway (iHS and XPEHH only).
Normal function is to disregard the score for that core.
Default: false

Speed improvements + TPED format support

15SEPT2014 - XP-EHH calculations in 1.0.2 are broken. Do not use 1.0.2 for XP-EHH calculations. Versions 1.0.0-1.0.1 and 1.0.3 calculate XP-EHH correctly.

General speed improvements have been made, especially with threading.

New support for TPED formatted files and a few new command line options are available:

--skip-low-freq : Do not include low frequency variants in the construction of haplotypes (iHS only).
Default: false

--max-extend : The maximum distance an EHH decay curve is allowed to extend from the core.
Set <= 0 for no restriction.
Default: 1000000

--tped : A TPED file containing haplotype and map data.
Variants should be coded 0/1
Default: __hapfile1

--tped-ref : A TPED file containing haplotype and map data.
Variants should be coded 0/1. This is the 'reference'
population for XP-EHH calculations and should contain the same number
of loci as the query population. Ignored otherwise.
Default: __hapfile2

Minor bug fixes

--XPEHH output header is now separated by tabs instead of spaces.
--Removed references to missing data (which is not accepted), and introduced error checking in the event of non-0/1 data being provided.

Initial release

Initial release of selscan and norm