Added workaround for odd-bam behaviour and full-contig search.
Added workaround for odd-bam behaviour and full-contig search.

jeromekelleher/ga4gh-streaming-tester,AlexanderVi/ga4gh-streaming-tester,AlexanderVi/ga4gh-streaming-tester,jeromekelleher/ga4gh-streaming-client,jeromekelleher/ga4gh-streaming-tester