Handle incremental addition of new lanes when dealing with multiple sequencing libraries

[vinjana]

Sooner or later we have to remove the per lane, and per library bam files and only keep the final merged bam file. Therefore, whenever a new lane for a specific library is sequenced, the aligned reads for that library have to be extracted from the merged bam file, and the newly aligned lane has to merged and duplicate marked against the library bam file and later merged into the final bam file.