fixing slowness in pysam_0.8.X

bqual = read.alignment.query_qualities[qpos] added

bug fixed in plotting BAF heatmap

1.4.2

Update README.md

Pysam_0.8X supported

fix the read.qpos => read.query_position change from Pysam_0.7X to Pysam_0.8X

Whole exome sequencing (WES) supported

New analysis pipeline for WES data is included based on DNAcopy segmentation.

matplotlib now optional

matplotlib is now optional;
example data link is added.

minor bugs fixed

BICseq2bed.py now supports ENSEMBL

bugs fixed

Update README.md

--WES added

supplementary figures changed

On branch master

README.md 1.1.2 -> 1.1.3
supplementary figures changed

manuscript/supplementary_data included

On branch master

README.md 1.1.1 -> 1.1.2

revision incorporated

ENSEMBLE chromosome format supported;