v2.8.0 BamCountRefs expanded

• Coverage bredth, RPKM, TPM, mean and counts outputs in bamcountsrefs

v2.7.0

• bamtocounts now supports --paired to count fragments
• bamtocounts fixed a bug that ignored the user flag to exclude
• [EXPERIMENTAL] testing --extendRead INT in bamtocov #6

v2.6.1 bugfix

• Compilation settings fixed to prevent crashes on certain systems

v2.6.0

• bamtocounts algorithm rewritten to accept unsorted and non-indexed files. the requirement for indexed files will be permanently dropped, for consistency across the suite, while we recommend using sorted files, and, in the future, this requirement might be added again to allow for performance gains.

v2.5.0 - Counts

• BamToCounts now uses the shared methods from BamToCov to manage the target (initially it used Lapper)

v2.4.0 - Stranded Wiggles

• Added support for --stranded analysis and Wiggle-like output (an extra column will be printed)

v2.3.0 Wig Output

• Improved Wig output
• Added Makefile
• Improved test suite

v2.2.0

• Experimental Wig output

v2.1.0

config-compile

2.0.4

v2.0.4

2.0.4