1. Fixed a major memory leak when using -sorted. Thanks to Emily Tsang and Stephen Montgomery.
2. Fixed a bug for BED files containing a single record with no newline. Thanks to @jmarshall.
3. The getfasta tool includes name, chromosome and position in fasta headers when the -name option is used. Thanks to @rishavray.
4. Fixed a bug that now forces the coverage tool to process every record in the -a file.
5. Fixed a bug preventing proper processing of BED files with consecutive tabs.
6. VCF files containing structural variants now infer SV length from either the SVLEN or END INFO fields. Thanks to Zev Kronenberg.
7. Resolve off by one bugs when intersecting GFF or VCF files with BED files.
8. The shuffle tool now uses roulette wheel sampling to shuffle to -incl regions based upon the size of the interval. Thanks to Zev Kronenberg and Michael Imbeault.
9. Fixed a bug in coverage that prevented correct calculation of depth when using the -split option.
10. The shuffle tool warns when an interval exceeds the maximum chromosome length.
11. The complement tool better checks intervals against the chromosome lengths.
12. Fixes for stddev, min, and max operations. Thanks to @jmarshall.
13. Enabled stdev, sstdev, freqasc, and freqdesc options for groupby.
14. Allow -s and -w to be used in any order for makewindows.
15. Added new -bedOut option to getfasta.
16. The -r option forces the -F value for intersect.
17. Add -pc option to the genomecov tool, allowing coverage to be calculated based upon paired-end fragments.