v0.5.0

Special shoutout to @Joon-Klaps for adding all new features in this release!

New features

1. Added duplicateReadCount to the getStatistics() method.
2. Added support for references on S3.
3. Added a gitpod yaml file.

Changes

1. Updated the docs to make the use of the sam and cram functions more clear

v0.4.0

New features

1. Added a new getStatistics() method to some general statistics:
   • minReadLength: The lowest read length
   • maxReadLength: The highest read length
   • meanReadLength: The mean read length
   • minMappingQuality: The lowest mapping quality
   • maxMappingQuality: The highest mapping quality
   • meanMappingQuality: The mean mapping quality
   • readCount: The amount of reads present in the file

v0.3.0

New features

1. Added the stringency option to the bam() function and all its aliases. This option takes lenient, silent and strict(default) as possible values and is used to set the validation stringency of the HTSJDK library.

0.2.0

New features

Added some new methods:

1. getHeaderMD5(): Returns the MD5 checksum of the header
2. getReadsMD5(): Returns the MD5 checksum of the raw reads
3. getSamLinesMD5(): Returns the MD5 checksum of the plain SAM lines

v0.1.1

Fixes

1. Recompiled the plugin with a lower version of htsjdk to ensure functionality on lower Java versions

v0.1.0

The first release of nft-bam 🥳

⚠️ This is a beta release ⚠️