1.2.1

• Fixed bug (#36 ) if deletion at final position of primer region.
• BED file (-b) now optional for ivar trim. In absence of BED file, ivar trim just does quality trimming and writes all reads that pass min length threshold (-m) to file. Fixes #35.
• should fix maybe-uninitialized errors
• ivar trim now supports unpaired reads

1.2

• Check and ignore unmapped reads
• Updated default consensus to -m 1 -n N
• Check BED file format
• GFF3 lines with # ignored
• Handle overlapping primers by taking minimum of start pos of primers for reverse reads and maximum of end position of primers for forward reads.
• Added more logging for trim and consensus

Version 1.1

• variants command includes minimum depth threshold
• variants command does amino acid translation using GFF file while account for polymerase slippage using EditPosition and EditSequence from the attributes column.
• filtervariants command filters variants based on minimum percentage threshold. Refactored into C++. No more awk script.

Verion 1.0.1

• Discarded quality checks for INDELS.
• Added -e flag to allow reads without primers to go through.

Version 1.0

iVar v1.0 has the following functions.

• Trimming primer sequences and low quality
• Call variants
• Filter variants across replicates
• Call a consensus sequence
• Get primer names with mismatches
• Remove reads selectively based on primer sequences