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Releases: andersen-lab/ivar

v1.4.3

21 Jun 02:16
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  • Issue #102 and #175 fix: Addresses issues with incorrect read start position, after trimming unpaired reverse reads.
  • Issue #180 fixed by @asereewit: Takes strand from GFF file into account for amino acid translation.
  • Dockerfile update to provide support for MacOs with ARM64, bumped ubuntu version from 18.04 to 20.04 as seen in Issue #165

v1.4.2

28 Mar 23:24
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What's Changed

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

v1.4.1

21 Mar 16:19
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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

25 Feb 01:35
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  • 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

06 Feb 20:39
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What's Changed

New Contributors

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

1.3.1

06 Feb 01:43
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  • 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

06 Nov 22:26
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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

02 Sep 19:53
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  • New flag QC FAIL to ivar trim
  • -i option to name FASTA header in ivar consensus
  • Bug fixes for memory leaks.

1.2.2

23 Apr 22:08
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  • Fixes #42 specifically for unpaired reads that span only 1 primer.
  • Removes uninitialized errors with gcc9

1.2.1

21 Apr 06:25
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  • 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