v1.4.2

What's Changed

• fix for ivar trim hanging with -f parameter by @cmaceves in #160
• update ubuntu images by @cmaceves in #161

Full Changelog: v1.4.1...v1.4.2

v1.4.1

What's Changed

• Fixed issues with streaming/piping for ivar trim functionality by addressing a bug in the use/setting of the -m parameter

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

v1.3.2

What's Changed

• Issue 79 by @cmaceves in #117
• Implementing more efficient sort method. by @cmaceves in #118
• issue 40 by @cmaceves in #122
• Issue 123 by @cmaceves in #127
• addressing issue #120 fix deletion post primer by @cmaceves in #124
• call_consensus_pileup.h: fix build failure with Gcc 12 by @emollier in #136
• Fix compilation on newer gcc versions by @JacobHayes in #141
• addressing issue #132 by @cmaceves in #137
• Solving compile errors for macos by @cmaceves in #146

New Contributors

• @cmaceves made their first contribution in #117
• @emollier made their first contribution in #136
• @JacobHayes made their first contribution in #141

Full Changelog: v1.3.1...v1.3.2

1.3.1

• ivar trim now has -x flag to specify an offset to search for primer positions. This allows for trimming of primer sequences with sequencing artifacts.

1.3

• ivar trim now has -k flag to mark all reads that fail filters as BAM_FQCFAIL and write to output BAM.
• ivar trim now considers reads with insert size less than read length as unpaired and trims both forward and reverse primers in these cases. Details in issue #73
• ivar trim will exclude paired end sequencing reads from aberrant amplicons that cross the expected amplicon boundaries. Details in issue #75

1.2.3

• New flag QC FAIL to ivar trim
• -i option to name FASTA header in ivar consensus
• Bug fixes for memory leaks.

1.2.2

• Fixes #42 specifically for unpaired reads that span only 1 primer.
• Removes uninitialized errors with gcc9

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