shift
Like fill, this is a very simple program. A value, N, must be specified and the data is shifted by N to all of the coordinates. N may be a negative number. Chromosome sizes stay the same as in the original bigWig, so data is clipped if it moves past the first or last base on the chromosome.
Usage message:
bwtool shift - move the data on the chromosome by N number of bases
usage:
bwtool shift N input.bw[:chr:start-end] output.bw
The typical example:
with the data being:
variableStep chrom=chr span=1
1 1
2 2
3 5
4 6
5 5
6 3
7 3
8 5
9 5
10 5
11 6
12 6
13 0
14 2
15 3
16 3
17 10
18 4
19 4
20 2
21 2
22 2
23 1
variableStep chrom=chr span=1
28 2
29 3
30 4
31 6
32 6
33 4
34 4
35 4
36 2
We can shift it all upstream 10 bases:
$ bwtool shift -10 main.bigWig shifted.bigWig -wigtype=var
$ bigWigToWig shifted.bigWig /dev/stdout
variableStep chrom=chr span=1
1 6
2 6
3 0
4 2
5 3
6 3
7 10
8 4
9 4
10 2
11 2
12 2
13 1
variableStep chrom=chr span=1
18 2
19 3
20 4
21 6
22 6
23 4
24 4
25 4
26 2
And we can shift it the other way as well:
$ bwtool shift 10 main.bigWig shifted.bigWig -wigtype=var
$ bigWigToWig shifted.bigWig /dev/stdout
variableStep chrom=chr span=1
11 1
12 2
13 5
14 6
15 5
16 3
17 3
18 5
19 5
20 5
21 6
22 6
23 0
24 2
25 3
26 3
27 10
28 4
29 4
30 2
31 2
32 2
33 1