Run performance tests

[apmasell]

Write some queries and test them compared to samtools view for accuracy and performance. Put them in the documentation as examples.

[apmasell]

For comparison:

time ./barf  -o barf_output.bam -b -f input.bam 'chr(M) | mate_chr(M)'

versus

samtools view -h input.bam | awk '/^@/ { print; header++; } $3 ~ /^(chr)?(M|25)$/ || $7 ~/^(chr)?(M|25)$/ {print; accepted++;} END { print "Accepted: " accepted " Rejected: " (NR- accepted-header) > "/dev/stderr" }' | samtools view -S -b -o foo2.bam -

The number of sequences accepted both say 7041512, the number rejected, both say 3955753362.

Variable	BARF	SAMtools+AWK
Time	3:31:41	4:04:01
File size	695344044	695250018

The file size different is larger than expected. There's a header addition, but it shouldn't be 91kB.