Code:
grep MATESW *.c
You'll see that it occurs when a read is fixed due to paired end rescue. Also, don't double post.
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Trysince 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. -
what does "XT:M" in BWA output mean?
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 3Last edited by orionzhou; 11-13-2010, 08:08 PM.
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