RagTag v2.1.1

Bug fix

• merge_alns(careful_merge=True) did not merge collinear reverse-strand alignments when the first alignment spanned more than merge_dist on the query (#213, #214). This problem can cause a wrong query orientation in ragtag scaffold, also when most of the aligned sequence is on the reverse strand. The problem started in v2.1.0.

Changes to the output

For query sequences with alignments on the reverse strand, the primary alignment can change. Thus, ragtag scaffold can give a different orientation, order, containment result, or inferred gap size (-r) for these sequences. ragtag correct and ragtag patch also use the careful merge, so their output can change too.

Tests

This release adds unit tests in tests/test_contig_alignment.py. Run them from the repository root with python -m unittest tests.test_contig_alignment.