Add sample_index to VariantHeader (analogous to field_index)
Merge pull request #304 from broadinstitute/jt_vh_sample_index

Add sample_index to VariantHeader (analogous to field_index)
Remove ycm extra configuration files
forgotten case
Merge pull request #312 from broadinstitute/ak_fix_samples_to_include_in_variant_reader

fix for forgotten list of samples to include
Merge pull request #309 from broadinstitute/mc_remove_ycm_files

Remove ycm extra configuration files
Read group class

Read group class

Minor changes base don code review

Minor improvements in code readabiity