bedtools 2.18 timing comparisons with 2.17 and bedops

comparo.txt

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# Version 2.18.0
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# BAM, CHROMSWEEP
time ./bedtools intersect -a random.20M.sorted.bam -b gencode.v17.exons.sorted.bed -sorted > /dev/null

real  0m20.153s
user	0m19.953s
sys	0m0.192s

# BAM, BINTREE
time ./bedtools intersect -a random.20M.sorted.bam -b gencode.v17.exons.sorted.bed > /dev/null

real	0m26.114s
user	0m25.562s
sys	0m0.544s


# BED, CHROMSWEEP
time ./bedtools intersect -a random.20M.sorted.bed -b gencode.v17.exons.sorted.bed -sorted > /dev/null

real	0m10.626s
user	0m10.397s
sys	0m0.220s


# BED, BINTREE
time ./bedtools intersect -a random.20M.sorted.bed -b gencode.v17.exons.sorted.bed > /dev/null

real	0m15.747s
user	0m15.137s
sys	0m0.600s


# PIPED BED, CHROMSWEEP
time cat random.20M.sorted.bed | ./bedtools intersect -a - -b gencode.v17.exons.sorted.bed -sorted > /dev/null

real	0m18.833s
user	0m18.445s
sys	0m0.760s


# PIPED BED, BINTREE
time cat random.20M.sorted.bed | ./bedtools intersect -a - -b gencode.v17.exons.sorted.bed > /dev/null

real	0m23.558s
user	0m22.829s
sys	0m1.100s

# COMPRESSED BED, CHROMSWEEP
time ./bedtools intersect -a random.20M.sorted.bed.gz -b gencode.v17.exons.sorted.bed -sorted > /dev/null

real	0m14.345s
user	0m14.217s
sys	0m0.120s


# COMPRESSED BED, BINTREE
time ./bedtools intersect -a random.20M.sorted.bed.gz -b gencode.v17.exons.sorted.bed > /dev/null

real	0m19.614s
user	0m19.097s
sys	0m0.508s



######################################################################################################
# Version 2.17.0
######################################################################################################

# BAM, CHROMSWEEP
time ~/cphg-quinlan/shared/bin/bedtools intersect -abam random.20M.sorted.bam -b gencode.v17.exons.sorted.bed -sorted > /dev/null

N/A


# BAM, BINTREE
time ~/cphg-quinlan/shared/bin/bedtools intersect -abam random.20M.sorted.bam -b gencode.v17.exons.sorted.bed > /dev/null

real	3m16.108s
user	3m15.896s
sys	0m0.156s


# BED, CHROMSWEEP
time ~/cphg-quinlan/shared/bin/bedtools intersect -a random.20M.sorted.bed -b gencode.v17.exons.sorted.bed -sorted > /dev/null

real	0m45.011s
user	0m44.615s
sys	0m0.380s


# BED, BINTREE
time ~/cphg-quinlan/shared/bin/bedtools intersect -a random.20M.sorted.bed -b gencode.v17.exons.sorted.bed > /dev/null

real	1m7.100s
user	1m6.216s
sys	0m0.860s


# PIPED BED, CHROMSWEEP
time cat random.20M.sorted.bed | ~/cphg-quinlan/shared/bin/bedtools intersect -a - -b gencode.v17.exons.sorted.bed -sorted > /dev/null

real	1m10.635s
user	1m10.180s
sys	0m0.832s


# PIPED BED, BINTREE
time cat random.20M.sorted.bed | ~/cphg-quinlan/shared/bin/bedtools intersect -a - -b gencode.v17.exons.sorted.bed > /dev/null

real	1m33.371s
user	1m32.774s
sys	0m1.024s

# COMPRESSED BED, CHROMSWEEP
time ~/cphg-quinlan/shared/bin/bedtools intersect -a random.20M.sorted.bed.gz -b gencode.v17.exons.sorted.bed -sorted > /dev/null

real	0m51.890s
user	0m51.779s
sys	0m0.092s


# COMPRESSED BED, BINTREE
time ~/cphg-quinlan/shared/bin/bedtools intersect -a random.20M.sorted.bed.gz -b gencode.v17.exons.sorted.bed > /dev/null

real	1m13.370s
user	1m13.137s
sys	0m0.208s





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# BEDOPS
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# basic bedmap
time ~/cphg-quinlan/shared/bin/bedmap --echo-map --bp-ovr 1 random.20M.sorted.bed gencode.v17.exons.sorted.bed > /dev/null

real	0m11.184s
user	0m11.089s
sys	0m0.088s

# bedmap add error checking
time ~/cphg-quinlan/shared/bin/bedmap --echo-map --bp-ovr 1 --ec random.20M.sorted.bed gencode.v17.exons.sorted.bed > /dev/null

real	0m16.187s
user	0m16.045s
sys	0m0.128s

# bedmap fast mode
time ~/cphg-quinlan/shared/bin/bedmap --echo-map --bp-ovr 1 --faster random.20M.sorted.bed gencode.v17.exons.sorted.bed > /dev/null

real	0m11.047s
user	0m10.941s
sys	0m0.100s

# bedops --intersect
time ~/cphg-quinlan/shared/bin/bedops --intersect random.20M.sorted.bed gencode.v17.exons.sorted.bed > /dev/null

real	0m9.188s
user	0m9.129s
sys	0m0.052s

# STARCH: bedops --intersect
time ~/cphg-quinlan/shared/bin/bedops --intersect random.20M.sorted.bed gencode.v17.exons.sorted.bed > /dev/null

real	0m43.144s
user	0m43.111s
sys	0m0.016s

# STARCH: basic bedmap
time ~/cphg-quinlan/shared/bin/bedmap --echo-map --bp-ovr 1 random.20M.sorted.bed.starch gencode.v17.exons.sorted.bed.starch > /dev/null

real	0m49.916s
user	0m49.867s
sys	0m0.032s