NAME

       reapr-score - calculate scores and assembly errors

SYNOPSIS

       reapr score [options] <assembly.fa.gaps.gz> <in.bam> <statsprefix> <FCDcutoff> <outprefix>

OPTIONS

       -f <int>
           Minimum inner fragment coverage [1]

       -g <int>
           Max gap length to call over [0.5 * outer_mean_insert_size]

       -l <int>
           Length of window [100]

       -p <int>
           Use perfect mapping reads score with given min coverage. Incompatible with -P.

       -P <int>
           Same as -p, but force the score to be zero at any position with at least the given
           coverage of perfect mapping reads and which has an OK insert plot, , i.e. perfect
           mapping reads + insert distribution override all other tests when calculating the
           score. Incompatible with -p.

       -q <float>
           Max bad read ratio [0.33]

       -r <int>
           Min read coverage [max(1, mean_read_cov - 4 * read_cov_stddev)]

       -R <int>
           Repeat calling cutoff. -R N means call a repeat if fragment coverage is >= N times
           (expected coverage). Use -R 0 to not call repeats [2]

       -s <int>
           Min score to report in errors file [0.4]

       -u <int>
           FCD error window length for error calling [insert_size / 2]

       -w <float>
           Min percentage of bases in window needed to call as bad [0.8]

SEE ALSO

       reapr(1)

                                                                                   REAPR-SCORE(1)