$ git clone https://github.com/tombch/basecount.git $ cd basecount/ $ conda env create -f environment.yml $ conda activate basecount $ pip install . 

$ basecount BAM_FILE 

reference position coverage num_a num_c num_g num_t num_ds pc_a pc_c pc_g pc_t pc_ds entropy secondary_entropy XXXXXXXXXX 1 0 0 0 0 0 0 -1 -1 -1 -1 -1 1 1 XXXXXXXXXX 2 0 0 0 0 0 0 -1 -1 -1 -1 -1 1 1 XXXXXXXXXX 3 0 0 0 0 0 0 -1 -1 -1 -1 -1 1 1 XXXXXXXXXX 4 0 0 0 0 0 0 -1 -1 -1 -1 -1 1 1 XXXXXXXXXX 5 0 0 0 0 0 0 -1 -1 -1 -1 -1 1 1 XXXXXXXXXX 6 0 0 0 0 0 0 -1 -1 -1 -1 -1 1 1 XXXXXXXXXX 7 0 0 0 0 0 0 -1 -1 -1 -1 -1 1 1 XXXXXXXXXX 8 0 0 0 0 0 0 -1 -1 -1 -1 -1 1 1 XXXXXXXXXX 9 0 0 0 0 0 0 -1 -1 -1 -1 -1 1 1 XXXXXXXXXX 10 0 0 0 0 0 0 -1 -1 -1 -1 -1 1 1 XXXXXXXXXX 11 0 0 0 0 0 0 -1 -1 -1 -1 -1 1 1 XXXXXXXXXX 12 0 0 0 0 0 0 -1 -1 -1 -1 -1 1 1 XXXXXXXXXX 13 0 0 0 0 0 0 -1 -1 -1 -1 -1 1 1 XXXXXXXXXX 14 0 0 0 0 0 0 -1 -1 -1 -1 -1 1 1 XXXXXXXXXX 15 0 0 0 0 0 0 -1 -1 -1 -1 -1 1 1 XXXXXXXXXX 16 0 0 0 0 0 0 -1 -1 -1 -1 -1 1 1 XXXXXXXXXX 17 0 0 0 0 0 0 -1 -1 -1 -1 -1 1 1 XXXXXXXXXX 18 0 0 0 0 0 0 -1 -1 -1 -1 -1 1 1 XXXXXXXXXX 19 0 0 0 0 0 0 -1 -1 -1 -1 -1 1 1 XXXXXXXXXX 20 0 0 0 0 0 0 -1 -1 -1 -1 -1 1 1 XXXXXXXXXX 21 1 0 1 0 0 0 0.0 100.0 0.0 0.0 0.0 0.0 1 XXXXXXXXXX 22 1 1 0 0 0 0 100.0 0.0 0.0 0.0 0.0 0.0 1 XXXXXXXXXX 23 1 0 0 1 0 0 0.0 0.0 100.0 0.0 0.0 0.0 1 XXXXXXXXXX 24 3 0 1 2 0 0 0.0 33.333 66.667 0.0 0.0 0.395 0.0 XXXXXXXXXX 25 1334 0 0 0 1334 0 0.0 0.0 0.0 100.0 0.0 0.0 1 XXXXXXXXXX 26 1396 1396 0 0 0 0 100.0 0.0 0.0 0.0 0.0 0.0 1 XXXXXXXXXX 27 1411 1411 0 0 0 0 100.0 0.0 0.0 0.0 0.0 0.0 1 XXXXXXXXXX 28 1429 0 1427 0 2 0 0.0 99.86 0.0 0.14 0.0 0.007 0.0 XXXXXXXXXX 29 1465 1453 0 1 0 11 99.181 0.0 0.068 0.0 0.751 0.031 0.207 XXXXXXXXXX 30 1472 1471 0 1 0 0 99.932 0.0 0.068 0.0 0.0 0.004 0.0 XXXXXXXXXX 31 1478 1464 1 13 0 0 99.053 0.068 0.88 0.0 0.0 0.035 0.186 XXXXXXXXXX 32 1482 0 1479 0 2 1 0.0 99.798 0.0 0.135 0.067 0.01 0.459 XXXXXXXXXX 33 1483 1 1479 0 3 0 0.067 99.73 0.0 0.202 0.0 0.013 0.406 XXXXXXXXXX 34 1483 1482 0 1 0 0 99.933 0.0 0.067 0.0 0.0 0.003 0.0 XXXXXXXXXX 35 1483 1481 0 2 0 0 99.865 0.0 0.135 0.0 0.0 0.006 0.0 XXXXXXXXXX 36 1484 0 1480 0 2 2 0.0 99.73 0.0 0.135 0.135 0.013 0.5 XXXXXXXXXX 37 1485 0 1485 0 0 0 0.0 100.0 0.0 0.0 0.0 0.0 1 XXXXXXXXXX 38 1485 1485 0 0 0 0 100.0 0.0 0.0 0.0 0.0 0.0 1 XXXXXXXXXX 39 1485 1483 0 2 0 0 99.865 0.0 0.135 0.0 0.0 0.006 0.0 : 

$ basecount BAM_FILE --summarise 

reference_name XXXXXXXXXX reference_length 29903 num_reads 123901 pc_reference_coverage 99.057 avg_depth 1649.805 avg_entropy 0.116 

$ basecount BAM_FILE --summarise-with-bed BED_FILE 

reference_name XXXXXXXXXX reference_length 29903 num_reads 123901 pc_reference_coverage 99.057 avg_depth 1649.805 avg_entropy 0.116 mean_coverage_amplicon_vector 243.906, 1229.481, 1729.518, 2711.367, 1346.401, 3041.555, 1309.193, 143.864, 1494.996, 42.. median_coverage_amplicon_vector 138.0, 1219.0, 1725.0, 2582.0, 678.0, 2932.0, 1309.0, 13.0, 1496.0, 16.0, 1471.0, 1644.0, .. mean_entropy_amplicon_vector 0.107, 0.116, 0.127, 0.118, 0.113, 0.111, 0.11, 0.077, 0.12, 0.071, 0.105, 0.119, 0.088, 0.. median_entropy_amplicon_vector 0.094, 0.104, 0.112, 0.102, 0.108, 0.101, 0.104, 0.0, 0.113, 0.013, 0.093, 0.111, 0.022, 0.. mean_secondary_entropy_amplicon_vector 0.437, 0.724, 0.702, 0.724, 0.69, 0.714, 0.709, 0.666, 0.713, 0.685, 0.735, 0.724, 0.666, .. median_secondary_entropy_amplicon_vector 0.485, 0.739, 0.714, 0.749, 0.729, 0.746, 0.736, 1.0, 0.737, 0.899, 0.753, 0.736, 0.953, 0.. 

$ basecount --help