Example for Newbler (with 1999 bp upper limit, i.e. strictly < 2000 bp)
Script to drop SAM reads with very long CIGAR strings

This is a workarround for the BAM/samtools limitation to 65535
operations in a CIGAR string, see also:
https://github.com/samtools/samtools/pull/39

SAM files from MIRA v4 used in mapping mode tend to have these
long CIGAR strings for back-bone reads.
Command line script for creating/checking Biopython's SeqIO index files