CHANGE HISTORY
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07-01-2007 v0.0.1
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First version

09-01-2007 v0.0.2
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-position of SNP in info file printed in fixed format rather than scientific.
-slightly cleaned up screen output. Now lists #SNPs in buffer regions and estimates RAM required.
-README file updated to include description of warning messages

11-01-2007 v0.0.3
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-added option to select SNPs that are output (default is all SNPs)
use -os 1 for SNPs with no genotypes i.e HapMap SNPs not on chip
use -os 2 for SNPs with both genotypes and haplotypes i.e. HapMap SNPs on chip
use -os 3 for SNPs with only genotypes i.e. SNPs on chip but not in HapMap
You can mix options i.e. -os 1 2 would output SNPs in the panel i.e. all HapMap SNPs

12-01-2007 v0.0.4
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-If output options specify that SNPs with no genotypes are not required in output then these SNPs are removed from the data structure at the start to save computation. This considerably speeds things up.
-bug in info file output fixed.

15-01-2007 v0.0.5
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-added check for haplotype SNPs in specified interval. exits if zero.

15-01-2007 v0.0.6
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-bug fixed in setup function

16-01-2007 v0.0.7
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-added genotype probabilities to SNP structure for Niall's use


19-01-2007 v0.0.8
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-changed precision of output to reduce size of files


20-01-2007 v0.0.9
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-bug fixed in memory estimation



05-02-2007 v0.1.0
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-added -exclude_snps option to exclude snps from imputation


05-02-2007 v0.1.1
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-changed how exclusion of snps is carried out. This is now done in a separate step at the end of the read_data function.


26-07-2007 v0.2.0
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-for SNPs with genotype data but no haplotype data the original genotypes are now returned. In the old version a uniform distribution on all genotypes was returned.
-fixed bug in forward calculation row and column sum calculation.
-added FD conditionals
-speed increase for LS calculations and reduced memory requirements
-added inclusion list option for haplotype ony SNPs
-fixed bug in screen output that list which snps will be in output
-removed rule that exclude snps fle shouldn't have an EOL on the last line.
-added check for number of SNPs to be in output. If =0 then terminates
-added -outdp flag for precision of output (default =2)

03-12-2007 v0.3.0
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-added LICENCE file
-at SNPs which have been genotyped in your sample the default is now to return these genotypes in the output file. There is a -pgs flag (which stands for predict genotyped snps) which replaces the genotyped SNPs with their predictions.
-added to the ways in which strand alignment can be carried out. If a strand file is given then this the information in this file is applied first. Then a check is done to see if the strand can be determined from the allele labels and at A/T and G/C SNPs allele frequencies are checked to see which is the best alignment. Then finally all SNPs that not aligned after one or other of these steps are removed. A summary of this process is written to the screen. There are also -no_fix and -no_remove flags that turn off the allele label/frequency matching and the non-aligned SNP removal steps. 
-added -g_gz and -o_gz that specify that the genotype file (-g) and output file (-o) are gzipped respectively

17-12-2007 v0.3.1
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-fixed small bug in reporting of the number of SNPs that have their strands flipped due to allele-mismatch. Was reporting 0 and now reports correct number. 
-fixed bug in -g_gz option

18-01-2008 v0.3.2
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-fixed small bug in the feature added in v0.3.0 to align strand using allele labels and allele frequencies. The bug only affects A/T and G/C SNPs in which the order of the two alleles differs between the genotype file and the haplotype file.
-when using -o_gz add .gz extension to output file 

26-05-2008 v0.4.0
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-change to cephes cprob and newran libraries
-no_fix flag has been replaced by -fix_strand flag. Now by default the internal strand alignment is not carried out and must be invoked using the -fix_strand flag. 
-impute_excluded flag has been added which causes the output to contain imputed genotypes at SNPs which were excluded using the -exclude_snps option. 
-the software comes with new (larger) example files 
-the info files now contains the expected allele frequency and a measure of the observed statistical information assocaited with the allele frequency estimate. The Brier's score measure has been removed. 
-The screen output now finishes by reporting a breakdown of impution accuracy at SNPs which have genotypes in the input file. The imputed genotype probabilities are compared to genotype calls from the input genotype file. The distribution of the maximum imputed genotype calls are given. This allows the user to assess how well imputation is performing. The accuracy obtained on these SNPs is likely to be a good reflection of the accuracy of the imputation at other SNPs not in the genotype input file.
-The screen output now reports a fuller breakdown of the SNPs that will be in the output file.
-made -int compulsory

28-05-2008 v0.4.1
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-changed way strand file is read so that SNPs don't need to be arranged in the same order as in the genotypes file. This means a strand file can contain strand info on SNPs not in the genotypes file i.e. SNPs that may have been filtered out.

16-06-2008 v0.4.2
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-edited phys2gen function to return position 0 by default
-fixed bug in read_strand_file 
-added -r option to specify a file where screen output is copied (default ./summary)
-added a check for duplicate SNPs in genotype file

29-06-2008 v0.4.3
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-added functionality to handle X chromosome data

01-08-2008 v0.5.0
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-added support for X chromosome imputation with associated options -chrX, -Xpar and -sample

01-12-2008 v1.0.0
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-edits to setup() and read_data() functions.
-Added -orig_strand flag to revert output files to the original strand coding
-Added -haploid flag to treat genotype input file as haploid rather than diploid
-minor additions to debug screen output
- Changed the behaviour of the -pgs flag at Type 3 SNPs. Before the thresholded genotypes were returned at the SNPs. Now the original input probabilities are returned.
