Bugfix

ITDiscover v0.3.1

Primarily fixes an issue where fuzzy insertions could be misclassified as spacer-bearing calls.

Fixed

• Fuzzy ITD calling now follows the same general selection logic as exact calling, so spacer-bearing reads with mismatches in the copied segment still support the same underlying variant.
• Tie-breaking is now consistent across exact and fuzzy matching: longest copied segment first, then the most 5' reference start.

Added

• The HTML report now includes a CALL THRESHOLDS section and shows Insertion Start for each call.

Spacer Sequences

ITDiscover v0.3.0

Spacer Sequences

Added

• Spacer-aware ITD calls now preserve bases on both sides of the copied segment.
• The report now shows Insertion Start alongside tandem start, copied sequence, and spacer sequence.

Changed

• Exact ITD classification now chooses the longest exact copied FLT3 segment and, when tied, the most 5' source interval.
• The HTML report now colors tandem sequence, spacer sequence, and mismatches separately so spacer-aware calls are easier to inspect.

Fixed

• Fuzzy matching now respects the same 5' tie-breaking rule as exact matching.
• The report now distinguishes spacer bases from the copied segment instead of flattening them into one undifferentiated insertion.

Notes

• The new synthetic FLT3 data under tests/data/synthetic_flt3/ is designed to exercise default exact calls, spacer-containing calls, and fuzzy calls with different mismatch thresholds.

Fuzzy Calls and Primer Trimming

ITDiscover v0.2.0

This release includes fuzzy calls, primer trimming, and a cleaner HTML report.

Added

• Allow fuzzy IDT calls by setting --max-mismatches option
• Allow optional primer trimming with --forward-primer and --reverse-primer
• Primer trimming is applied before read filtering and ITD calling
• The HTML report now uses cleaner mismatch highlighting and simplified section titles

Removed

• The tabular ITD summary is no longer printed to stdout
• Numbered report headings like ITD 1, ITD 2, etc. were removed since they did not add useful information

Filtering

ITDiscover v0.1.1

This minor release is all about filtering of variants.

Added

• Allow setting --min-support-count and --min-vaf in CLI
• Filtering status is displayed in the HTML report

Removed

• The unique_support_count metric was at best a little confusing

First Release

ITDiscover v0.1.0

First functional release of ITDiscover for calling internal tandem duplications (ITDs) from amplicon sequencing data.

Added

• Exact-match calling from paired-end FASTQ input
• Flat CLI interface:
  • itdiscover --reference ... --r1 ... --r2 ...
• Call-level reporting of:
  • tandem start
  • insertion start
  • duplicated sequence
  • support count
  • unique support count
  • coverage
  • VAF
• HTML support report via --output report.html
• Representative-alignment reporting for unique support patterns
• Per-pattern support counts in the HTML report
• Base-level highlighting of differences between support representatives

Known limitations

• Exact-match ITD detection only in this release
• No fuzzy similarity-based ITD classification yet
• No extended annotation layer yet beyond current call/report output