* Allow for tracking of paired-end reads from bam input files * Add an option to use a scratch directory
0.11.0
* Change the input format to --input1 --input2 --unpaired * Trim the spaces in the identifiers sequences of the input files * Add the identifier sequence number if not present in the input files * Allow for files with less then N lines (in checks for sequence identifiers)
0.10.0
* Remove the file sort from the function that counts the reads so the file name and database name are always in sync. Resolves issue with workflows where read counts are out of sync for database names. * Change trimmomatic min read length to 60 nt. * Add back in legacy option "--run-trf" for backwards compatibility with workflows.
0.9.0
* Changed bowtie2 settings from --very-sensitive to --very-sensitive-local * Checking 1st and last 100 seq and removing spaces from seq identifiers if present * Add min len to start of trimmomatic run to try to resolve trimmomatic hanging during adapter trimming with short reads
0.8.0
* Add another bowtie2 option for filtering of paired end reads. This "strict" mode, the new default, removes both reads if either pair aligns. Modify existing pair alignment options into a single option.
0.7.10
* Remove trim-repetitive sequences option (prior set as default for filtering to remove adapters and overrepresented sequences). * Add more adapters plus option to select adapter type.