convertSAMToDataFrame

Convert a SAM or BAM file and convert to a in memory DataFrame, where the CIGAR strings are parsed into counts. This can produce a very large file if there is lots of sequences. To keep things managable, consider setting includeSequence to false or filter the reads. e.g. convertSAMToDataFrame("path/myFile.sam",false){NM<2 && numM 100} - would not include the sequence, and retain only sequences with less than two mismatches and matched for more than 100 bp.