v1.4

• Removed excess insertionSort calls in PR #155 to address speed issues in ivar trim from issue #154 and issue #147 introduced in previous version ivar 1.3.2.

• ivar trim now uses binary search to get overlapping primers (PR #155). This along with passing primers by reference to get_overlapping_primers() leads to a speedup of ~45% over ivar version 1.3.1.

• Default -m min_length setting for ivar trim is now set to 50% of the average length of the first 1000 reads as requested in issue #143

• Alignment file (Sorted/Unsorted SAM/BAM) can now be piped into ivar trim. Further, if no prefix using -p is specified, ivar trim will output trimmed SAM to stdout. This enables going from alignment to consensus using a one-liner. For example,
  bwa mem idx read1.fq reads2.fq | ivar trim -b test.bed -x 3 -m 30 | samtools sort - | samtools mpileup -aa -A -Q 0 -d 0 - | ivar consensus -p test_consensus -m 10 -n N -t 0.5