Refactor aln.cpp

[marcelm]

This renames:

• align_SE → align_single
• align_PE → align_paired
• align_SE_read → align_or_map_single
• align_PE_read → align_or_map_paired
• joint_nam_scores → nam_pairs (since we now use the NamPair struct)
• rescue_mate → rescue_align (could never remember what it does differently from rescue_read)
• Rename get_mapq to proper_pair_mapq (since this is only used to compute MAPQ for uniquely mapping proper pairs)

Also, InsertSizeDistribution is moved to a separate file.

The main change is to factor out an output_aligned_pairs() function. The rescue_read() and align_paired() functions previously did two things:

• Compute a list of paired alignments
• Output them to SAM

When working on random alignment selection for #367, I noticed that the code outputting to SAM was duplicated (and had slightly diverged already). This commit moves that part to a new function output_aligned_pairs(). Now rescue_read() and align_paired() just return a vector of ScoredAlignmentPairs.

This should fix at least two bugs:

• The details for R1 and R2 were swapped when R1 was rescued
• MAPQ of secondary alignments was inconsistently set to 0 or 255 depending on whether it was a rescued alignment or not.

[ksahlin]

I haven't had the time to look at all the changes in this PR in detail. But I agree with the name changes and with what you describe, without reservation.

If this PR is holding up any other development, or if you think its mostly non-controversial changes, I suggest a merge without a careful check.

[marcelm]

Do you want to review this PR more closely or shall I just merge it?

[ksahlin]

Won't have time anytime soon unfortunately . Yes please go ahead and merge.