Fix bam IO to take account of BAM_FPAIRED when checking BAM_FREAD1/2

This patch fixes bam IO to take account of BAM_FPAIRED when checking BAM_FREAD1/2.  According to the spec "If 0x1 is unset, no assumptions can be made about... 0x2, 0x8, 0x20, 0x40 and 0x80".