starts and ends should go to different files

[nsheff]

It seems the counting of number of bases output is off.

./uniwig test2.bed 1 5 | wigToBigWig stdin `refgenie seek hg19/fasta.chrom_sizes` out.bw
There's more than one value for chr11 base 50 (in coordinates that start with 1).

cat test2.bed
chr11   10      50
chr11   20      76

[nsheff]

yeah something's not right here. why would this example output 2 headers?

cat test3.bed
chr1    1       10
chr1    8       15
chr1    9       22

./uniwig test3.bed 1 0
fixedStep chrom=chr1 start=1 step=1
1
0
0
0
0
0
0
1
1
0
0
0
0
0
0
0
0
0
0
0
0
0
fixedStep chrom=chr1 start=10 step=1
0
0
0
0
0
0
0
0
0
1
0
0
0
0
1
0
0
0
0
0
0
1

[nsheff]

I see now. It appears to be spitting out the starts and then the ends right afterwards!

[nsheff]

So, starts and ends need to go to different files somehow.

It's nice that it prints to stdout, though, so I can just pipe to wigToBigWig. But that's not compatible with 2 outputs.

is there an efficiency gain in doing both at the same time? but then why is one printed after the other? If you're really going through the file twice, then I'd suggest just introducing CLI flags, --starts and --ends, and running it twice.

But there are efficiency gains to be had from doing them simultaneously, but then you have to print to 2 places. You can't do one after the other without retaining everything in memory. In that case I'd do --starts file.wig --ends file.wig. then you only have to go through the file once, and just print to 2 separate file handles as you go, for each start/end.