samtools view -bSu in pipe is now redundant

[tseemann]

FYI, the samtools view is not needed since version 1.3 (or earlier possibly)

java -jar build/libs/bazam.jar -bam my.bam | \
         bwa mem -p ref.fa  - | \
         samtools view -bSu - | \
         samtools sort -o out.bam 

Can be done as:

java -jar build/libs/bazam.jar -bam my.bam | \
         bwa mem -p ref.fa  - | \
         samtools sort > out.bam 

Much speed can be gained by using sort --threads X and --memory Xm too.

[ssadedin]

Thanks - will update docs!