changeset.txt

== Version 2.2.0
- added option "marker_counts" (by Nicola)

=== Version 2.1.0
- added min_alignment_len option to filter out short alignments in local mode. For long reads (>150) it is now recommended to use local mapping together with "--min_alignment_len 100" to filter out very short alignments. (by Tin)
- added "--samout" option to store the mapping file in SAM format (the SAM will be compressed if the extension of the specified output file ends with ".bz2") (by Tin)
- fix: MetaPhlAn2 now ingores about ~300 markers that were a-specific (thanks to Eric)

=== Version 2.0.0
- fix: Biom >= 2.0.0 has the clade IDs second and the sample ids third'
- added extract_markers.py
- fix: #5; revamp biom generation; set clade IDs as enumeration
- added utils/metaphlan2krona.py