1.0.3 Merge branch 'devel'

INSTALL

@@ -26,4 +26,4 @@ To build (some lines in the Makefile may need to be commented/uncommented):
 
 make norm 
 
-The norm binary will appear in the src/ directory when built.
+The norm binary will appear in the src/ directory when built.

README

@@ -21,9 +21,39 @@ BF Voight, et al. (2006) A map of recent positive selection in the human
 PC Sabeti, et al. (2002) Detecting recent positive selection in the human 
 	genome from haplotype structure. Nature, 419: 832–837.
 
+15SEP2014 - Release of 1.0.3.  **A critical bug in the XP-EHH module was introduced in version 1.0.2 and had 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 <bool>: 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
+
+17JUN2014 - Release of 1.0.2.  General speed improvements have been made, especially with threading.  New support for TPED formatted data and new command line options are available.
+
+--skip-low-freq <bool>: 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 <string>: A TPED file containing haplotype and map data.
+	Variants should be coded 0/1
+	Default: __hapfile1
+
+--tped-ref <string>: 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
+
+10APR2014 - Release of 1.0.1.  Minor bug fixes. XP-EHH 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.
+
+26MAR2014 - Initial release of selscan 1.0.0.
+
 USAGE:
 
-Data must be phased and have no missing genotypes.
+**Data must be phased and have no missing genotypes.**
 
 To calculate EHH:
 
@@ -72,16 +102,16 @@ selscan --xpehh --hap example2.pop1.hap --ref example2.pop2.hap --map example2.m
 
 ----------Command Line Arguments----------
 
---hap <string>: A hapfile with one row per haplotype, and one column per 
-	variant.  Variants should be coded 0/1.
+--hap <string>: A hapfile with one row per haplotype, and one column per
+	variant. Variants should be coded 0/1
 	Default: __hapfile1
 
---map <string>: A mapfile with one row per variant site.  
-	Formatted <chr#> <locusID> <genetic pos> <physical pos>. 
+--map <string>: A mapfile with one row per variant site.
+	Formatted <chr#> <locusID> <genetic pos> <physical pos>.
 	Default: __mapfile
 
---ref <string>: A hapfile with one row per haplotype, and one column per 
-	variant.  Variants should be coded 0/1. 	This is the 'reference' 
+--ref <string>: A hapfile with one row per haplotype, and one column per
+	variant. Variants should be coded 0/1. This is the 'reference'
 	population for XP-EHH calculations.  Ignored otherwise.
 	Default: __hapfile2
 
@@ -98,51 +128,56 @@ selscan --xpehh --hap example2.pop1.hap --ref example2.pop2.hap --map example2.m
 --out <string>: The basename for all output files.
 	Default: outfile
 
---ehh <string>: Calculate EHH of the '1' and '0' haplotypes at the specified 
-	locus.  Output: <physical dist> <genetic dist> <'1' EHH> <'0' EHH> 
-	Default: __NO_LOCUS__
-
---ihs <bool>: Set this flag to calculate iHS. 
+--ihs <bool>: Set this flag to calculate iHS.
 	Default: false
 
 --xpehh <bool>: Set this flag to calculate XP-EHH.
 	Default: false
 
---ehh-win <int>: When calculating EHH, this is the length of the window in bp 
+--ehh <string>: Calculate EHH of the '1' and '0' haplotypes at the specified
+	locus. Output: <physical dist> <genetic dist> <'1' EHH> <'0' EHH>
+	Default: __NO_LOCUS__
+
+--ehh-win <int>: When calculating EHH, this is the length of the window in bp
 	in each direction from the query locus.
 	Default: 100000
 
---cutoff <double>: The EHH decay cutoff.
-	Default: 0.05
+--max-gap <int>: Maximum allowed gap in bp between two snps.
+	Default: 200000
 
---gap-scale <int>: Gap scale parameter in bp.
-	If a gap is encountered between two snps > GAP_SCALE and < MAX_GAP, then 
-	the genetic distance is scaled by GAP_SCALE/GAP.
+--gap-scale <int>: Gap scale parameter in bp. If a gap is encountered between
+	two snps > GAP_SCALE and < MAX_GAP, then the genetic distance is
+	scaled by GAP_SCALE/GAP.
 	Default: 20000
 
---maf <double>: If a site has a MAF below this value, the program will not use 
-	it as a core snp.
+--cutoff <double>: The EHH decay cutoff.
 	Default: 0.05
 
---max-gap <int>: Maximum allowed gap in bp between two snps.
-	Default: 200000
-
 --max-extend <int>: The maximum distance an EHH decay curve is allowed to extend from the core.
 	Set <= 0 for no restriction.
 	Default: 1000000
 
+--maf <double>: If a site has a MAF below this value, the program will not use
+	it as a core snp.
+	Default: 0.05
+
 --skip-low-freq <bool>: Do not include low frequency variants in the construction of haplotypes (iHS only).
 	Default: false
 
---threads <int>: The number of threads to spawn during the calculation.  
-	Partitions loci across threads.
-	Default: 1
-
 --alt <bool>: Set this flag to calculate homozygosity based on the sum of the
-	squared haplotype frequencies in the observed data instead of using 
-	binomial coefficients. 
+	squared haplotype frequencies in the observed data instead of using
+	binomial coefficients.
 	Default: false
 
+--trunc-ok <bool>: 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
+
+--threads <int>: The number of threads to spawn during the calculation.
+	Partitions loci across threads.
+	Default: 1
+
 --help <bool>: Prints this help dialog.
 	Default: false
 

example/example.ehh.Locus4077.log

@@ -1,4 +1,4 @@
-../src/selscan --ehh Locus4077 --hap example.hap --map example.map --out example 
+selscan --ehh Locus4077 --hap example.hap --map example.map --out example 
 
 Calculating  iHS.
 Haplotypes filename: example.hap