what does "XT:M" in BWA output mean?

[orionzhou]

XT:U => Unique alignment
XT:R => Repeat
XT:N => Not mapped
XT:M => Mate-sw

so what the hell is this "Mate-sw" type alignment?

PS:
#define BWA_TYPE_NO_MATCH 0
#define BWA_TYPE_UNIQUE 1
#define BWA_TYPE_REPEAT 2
#define BWA_TYPE_MATESW 3

[nilshomer]

Try

grep MATESW *.c

since you already started searching through the source code.

You'll see that it occurs when a read is fixed due to paired end rescue. Also, don't double post.