some chroms are left out

[nsheff]

it appears that the chromosomes must be sorted in lexographical order rather than natural numeric chrom order, otherwise chromosomes are silently ignored.

For example, chr10 is ignored here:

databio/nsheff|~/code/uniwig$ cat test3.bed                                                                                        
chr1    7       10                                                                                                                 
chr1    8       12                                                                                                                 
chr1    9       15                                                                                                                 
chr9    4       7                                                                                                                  
chr10   2       3                                                                                                                  
                                                                                                                                   
databio/nsheff|~/code/uniwig$ ./uniwig test3.bed 1 1                                                                               
fixedStep chrom=chr1 start=7 step=1                                                                                                
1                                                                                                                                  
2                                                                                                                                  
3                                                                                                                                  
2                                                                                                                                  
1                                                                                                                                  
0                                                                                                                                  
0                                                                                                                                  
0                                                                                                                                  
0                                                                                                                                  
0                                                                                                                                  
fixedStep chrom=chr9 start=4 step=1                                                                                                
2                                                                             

if you move it before chr9, then it is included.