SAM file flags show reads not aligned properly

Sometimes a read shows up in prelim.csv with a flag without the 0x2 bit. This means that the read is not mapped in a proper pair. This flag is described in the manual (PDF) as, "each segment properly aligned according to the aligner".

The samtools mpileup command does not include reads in the pileup if this flag is not set, so we stopped including them in sam_to_conseq().

What exactly does this flag mean, and should we use the reads without this flag set? If we decide not to use them, filter them out of the remap.csv output, and check whether they need to get filtered anywhere else.

Start with sam_to_conseq() and the generation of prelim.csv and remap.csv. Read the linked SAM specification and Picard flag explanation, then trace where reads lacking 0x2 are handled and whether other outputs include them. Done means the flag behavior is understood, a filtering decision is recorded, and the affected outputs consistently follow it.