indel stuff

• indels: report length and bq-bin and add scripts/analyze-indel-errors.py to plot indel error rate
• combine_counts: better error messages and handle NA

v0.2.6

What's Changed

• add lua expressions to skip reads
• better error message when no bams are given
• fix reporting when neither read matches the reference
• Fix overflow when reporting stats for reads longer than 255 bp by @pontushojer in #12

New Contributors

• @pontushojer made their first contribution in #12

Full Changelog: v0.2.5...v0.2.6

respect include/exclude

• respect include and exclude for indels and denominator calculation (thanks Jason for reporting)

Full Changelog: v0.2.4...v0.2.5

bug-fixes

v0.2.4

• Allow chromosomes longer than u8::MAX (#11 thanks @pontushojer for reporting)
• Fix: when an include region was given and a non-seen chromosome was queried, it would return all intervals in that chromosome (#10 thanks Jason)

v0.2.3

more work on homopolymer distance

Full Changelog: v0.2.2...v0.2.3

fix homopolymer distance

Full Changelog: v0.2.1...v0.2.2

v0.2.1

This release adds tracking for distance of an error to a homopolymer (as defined by a user-regex).
It also optionally writes a denominator.bed file to see how many total overlapping read bases were sampled for each site.
Most information will be in the -counts.txt file.
The files output from this release will be incompatible with files from previous releases and this version of fraguracy will not work with files from previous releases.

Thanks to Jason K for driving the testing and features in this release.

Full Changelog: v0.1.9...v0.2.1

tracking indel errors

This release adds tracking of indel errors (differences between overlaps in paired-end reads). It outputs a separate bed file.

What's Changed

• track indel errors by @brentp in #5

Full Changelog: v0.1.8...v0.1.9

fix combine-errors

v0.1.8

fix combine-errors

better error messages

Full Changelog: v0.1.6...v0.1.7