Add support to force global / glocal / end-to-end alignment

[tseemann]

@lh3 Heng,

I am writing in the hope that you will consider adding a -g option to force global (really glocal, or end-to-end) alignment in BWA MEM.

I understand that BWA MEM currently will attempt to return a global alignment if the score is "close" to the best local alignment (based on the -L clipping penalties), otherwise prefers local alignment and puts soft clips in the SAM file.

There are cases where I want to force global alignment. For example, correcting an assembly with the same reads that generated the assembly, where naively passing BWA MEM output will sometimes result in false SNPs.

I had thought that just setting -L 99999,99999 might produce my desired behaviour, but it doesn't - probably due to the if (gscore <= 0 conditional in these lines:

https://github.com/lh3/bwa/blob/master/bwamem.c#L736
https://github.com/lh3/bwa/blob/master/bwamem.c#L764

I tried forcing that with a patch but it didn't seem to make a difference. My attempt was probably naive so I am hoping you can help / advise here!

Torsten

CC: @drpowell