Supplemental reads' primary component not filtered out

[cmatKhan]

callingCardsTools/callingcardstools/QC/create_status_coder.py

Line 92 in 033b541

read_details.get('read').is_supplementary:

This only removes the bam record which is labeled with flag 2048. However, there will be another record marked as the primary alignment and no supplemental flag.

The primary alignment will have a SA flag identifying the supplemental read if it has one -- check that the SA flag doesn't exist, also.

This affects the callingcards pipeline for both mammals and yeast