updated changelog in preparation for new release

Author: gmcvicker

CHANGELOG.md

@@ -1,3 +1,23 @@
+Version 0.2.2 - November 15, 2017
+-----------
+
+This release incorporates several modifications/fixes that have been made to
+the master branch over the past year.
+
+Changes include:
+* check first 2 bytes of input files to decide if they are gzipped rather than relying on .gz filename extension
+* fix bug in which unmapped reads in BAM were causing find_intersecting_snps.py to crash
+* fix bug in which some cigar codes caused find_intersecting_snps to crash because of typo in snptable
+* fix bug related to soft-clipped reads (switch to use pysam 'query_sequence' instead of 'query' attribute)
+* added check for pysam version to rmdup_pe and find_intersecting_snps.py
+* added check for pytables version to find_intersecting_snps.py
+* rescale count totals in CHT so that alpha and beta estimates stay in reasonable range
+* allow empty header lines in VCF parsing
+* change max SNP identifier length from 16 to 255
+* include much more information in output table from combined haplotype test such as SNP info, total numbers of AS reads, etc.
+* warn and gracefully handle situation where there are no matching samples on a chromosome
+
+
 Version 0.2.1 - September 5, 2016
 -----------
 This minor release corrects an issue where the cht_data module was not included in the v0.2 release. This module is required by the fit_bnb_coefficients.py script.