sambamba_161.d

// compilation: rdmd --build-only -O -release -inline -IBioD sambamba_161.d
// to use LDC: rdmd --compiler=ldmd2 [--force] ...
import bio.bam.reader, bio.bam.writer, std.parallelism;

void main(string[] args) {
  // boilerplate
  defaultPoolThreads = 8;
  auto input = new BamReader(args[1]); // use std.getopt for better args handling
  auto output = new BamWriter(args[2]);
  output.writeSamHeader(input.header);
  output.writeReferenceSequenceInfo(input.reference_sequences);
  scope(exit) output.finish();

  // filtering
  immutable threshold = 90; 
  foreach (read; input.reads) {
    // Warning: M corresponds to match/mismatch in BAM spec.
    // If you are interested only in matches, use
    // read.extended_cigar instead (requires ubiquitous MD tag)
    // and '=' operation type.
    uint total_len = 0;
    foreach (op; read.cigar)
      if (op.type == 'M')
        total_len += op.length;
    if (total_len > threshold)
      output.writeRecord(read);
  }
}