Merge pull request andersen-lab#88 from andersen-lab/swift_fix

added optional -x flag for ivar trim. allows trimming of reads that occur at a specified offset position relative to the primer sequence positions

Merge pull request andersen-lab#80 from andersen-lab/amplicon_search

Amplicon search

Merge pull request andersen-lab#80 from andersen-lab/amplicon_search

Amplicon search

Added input option to prompt

Fixed unsigned signed comparisons

Added test for unpaired reads

Updated version

Updated documentation

Added -e flag

Corrected reads without primer sequence message