Bamtocov

covtobed algorithm is being ported to Nim

Benchmarks

Human targeted sequencing of 16 genes (panel)

Command	Mean [ms]	Min [ms]	Max [ms]	Relative
bamtocov-2.0.2 "panel_01.bam"	505.8 ± 6.8	500.1	515.9	1.41 ± 0.07
bamtocov-2.0.4 "panel_01.bam"	409.6 ± 13.7	394.8	430.4	1.14 ± 0.07
bamtocov-2.1.0 "panel_01.bam"	390.1 ± 9.7	375.5	400.1	1.09 ± 0.06
bamtocov-2.1.0-nimble "panel_01.bam"	358.9 ± 18.3	341.6	387.9	1.00
bamtocov-2.1.0-nim "panel_01.bam"	436.0 ± 12.8	411.7	445.9	1.21 ± 0.07
covtobed-1.2 "panel_01.bam"	533.2 ± 8.8	527.1	548.4	1.49 ± 0.08
megadepth-1.1.2 --coverage "panel_01.bam"	9246.8 ± 1509.7	8026.7	11072.8	25.77 ± 4.41
mosdepth-0.3.1 /tmp/prefix "panel_01.bam"	53499.6 ± 875.1	52284.1	54548.5	149.08 ± 7.97

Human exome, subsampled, only Chromosome 2

Command	Mean [s]	Min [s]	Max [s]	Relative
bamtocov-2.0.2 "HG00258.04-chr2.bam"	36.281 ± 0.537	35.707	36.771	4.17 ± 0.06
bamtocov-2.0.4 "HG00258.04-chr2.bam"	43.611 ± 1.167	42.297	44.529	5.01 ± 0.14
bamtocov-2.1.0 "HG00258.04-chr2.bam"	43.888 ± 0.797	43.371	44.805	5.04 ± 0.09
bamtocov-2.1.0-nimble "HG00258.04-chr2.bam"	18.416 ± 0.863	17.465	19.149	2.12 ± 0.10
2.1.0-nimc "HG00258.04-chr2.bam"	43.696 ± 0.269	43.409	43.942	5.02 ± 0.03
covtobed-1.2 "HG00258.04-chr2.bam"	24.794 ± 0.469	24.340	25.278	2.85 ± 0.05
megadepth-1.1.2 --coverage "HG00258.04-chr2.bam"	8.706 ± 0.028	8.687	8.738	1.00
mosdepth-0.3.1 /tmp/prefix "HG00258.04-chr2.bam"	19.134 ± 1.330	17.609	20.056	2.20 ± 0.15