testing bedtools intersect with multiple database (-b) files

test.sh

# test each database file individually
time bedtools intersect -wa -wb -sorted \
                            -a hg19.rmsk.bed.gz \
                            -b hg19.segdup.bed.gz \
                            > /dev/null
real	0m5.069s
user	0m5.007s
sys	0m0.056s

time bedtools intersect -wa -wb -sorted \
                            -a hg19.rmsk.bed.gz \
                            -b hg19.CpG.bed.gz \
                            > /dev/null
real	0m4.872s
user	0m4.815s
sys	0m0.054s

time bedtools intersect -wa -wb -sorted \
                            -a hg19.rmsk.bed.gz \
                            -b hg19.gerp.elements.bed.gz \
                            > /dev/null
real	0m5.846s
user	0m5.776s
sys	0m0.067s

# now test all three at once.
time bedtools intersect -wa -wb -sorted \
                            -a hg19.rmsk.bed.gz \
                            -b hg19.segdup.bed.gz \
                               hg19.CpG.bed.gz \
                               hg19.gerp.elements.bed.gz \
                            > /dev/null
real	0m6.305s
user	0m6.226s
sys	0m0.074s

# test output. fifth column is the file number from which the hit came.
time bedtools intersect -wa -wb -sorted \
                            -a hg19.rmsk.bed.gz \
                            -b hg19.segdup.bed.gz \
                               hg19.CpG.bed.gz \
                               hg19.gerp.elements.bed.gz \
     | grep 223742388
chr1	223742388	223742413	Low_complexity_Low_complexity_GC_rich	1	chr1	223725644	223747846
chr1	223742388	223742413	Low_complexity_Low_complexity_GC_rich	2	chr1	223741965	223744525
chr1	223742388	223742413	Low_complexity_Low_complexity_GC_rich	3	chr1	223741996	223742814	1.8343e-32