Previous alignments of split reads are now removed before merging.
Previous alignments of split reads are now removed before merging.

With bma mem, it was possible to get alignments and secondary alignments to
the start and end of the reference sequence. Now we remove the alignments
in the linear bam file before merging the reads that were split across the
end and start of the sequence.

svohr/circ_aln,svohr/circ_aln