Changes

* Enabled writing log file by defalut. (11/18/2012)

* Enabled writing log file by defalut. (11/18/2012)

* Forced sample IDs to be matched when reading in kinship from a file. Perform a sanity check before reading in kinship file. If a sample of interest is not included in kinship file, then fatal error will occur. (11/19/2012)

* Forced sample IDs to be matched when reading in kinship from a file. Perform a sanity check before reading in kinship file. If a sample of interest is not included in kinship file, then fatal error will occur. (11/19/2012)

== Key Features ==

== Key Features ==

* prefix.traitName.singlevar.score.txt contains summary level statistics that are needed by Rare-Metal. An example is shown in below:

* prefix.traitName.singlevar.score.txt contains summary level statistics that are needed by Rare-Metal. An example is shown in below:

   LDL mean= -0.00, variance=  1.00, heritability= 34.30  

   LDL mean= -0.00, variance=  1.00, heritability= 34.30

   CHR POS REF_ALLELE ALT_ALLELE INFORMATIVE_N FOUNDER_AF ALL_AF INFORMATIVE_AC STAT ALT_ALLELE_EFFSIZE PVALUE

   CHR     POS     REF_ALLELE     ALT_ALLELE     INFORMATIVE_N   FOUNDER_AF     ALL_AF INFORMATIVE_AC HWE_PVALUE      STAT   ALT_ALLELE_EFFSIZE     PVALUE

   chr1 762320 G         A         6103         0.0038225 0.0038225 45 4.73428       0.0949001         0.502675

   chr10  45410002        G       A       6103   0.0341589      0.0341589       410    0.165893        126.205 0.309798        4.03074e-10

   chr1 865628 G         A         6103         0.00556756 0.00556756 67 18.3894       0.249333         0.0322511

   chr19  45412079        G       A       6103   0.0368124      0.0368124       434    0.714645        -265.84 -0.587356      7.87851e-36

  chr1 865665 G         A         6103         8.30979e-05 8.30979e-05 1 -0.740215    -0.599493         0.505316

   chr19  45414451        G       A      6103   0.444989        0.444989        5312    0.0759271      -26.1212        -0.00837122     0.640058

   chr1 878744 C         G         6103         0.00667334 0.00667334 80 -19.5138      -0.220432         0.0380796

  chr1 879381 G         A         6103         8.31117e-05 8.31117e-05 1 -0.831691     -0.61887         0.473108

* pvalues from the above output are from the family-based single variant score test.

* pvalues from the above output are from the family-based single variant score test.