Hi,

I'm running bam-readcount (commit `6c3f3ae901`) on a few hundred bam files against a single reference fasta file (designated with `-f`). However, when I look at the output for any of the files, all of the reference bases, for any position, are N.

    NODE_14_length_46_cov_1.239130  52      N       1       =:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00  A:1:2.00:36.00:2.00:1:0:0.00:0.02:0.00:0:0.00:0.00:0.00 C:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00    G:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00  T:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00  N:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00

Is this a bug? The base in the reference sequence at this position is A.

    >NODE_14_length_46_cov_1.239130
    AGCTAACTGAGTTTATCACACTCAGTTAATGTCCATTTCACTTCACACATAACCTTACAG
    ATCGGAAGATCTCGTA

Thanks!
I see this if I run on the entire BAM file without specifying a list of positions or a region. This is a bug. I pushed a very quick fix out that should solve this issue. It's 4b6479a42d002d855eda6a45bca097756d493cdb. Does this fix the issue?