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