Merge pull request #229 from dib-lab/fix/indel-snvs

Call SNVs near INDELs

CHANGELOG.md

@@ -22,13 +22,15 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 - Replaced `--ksize` with `--seed-size` in `kevlar localize` so that `kevlar alac` can now support different values for k-mers and localizing seeds/anchors (see #198).
 - Improved variant sorting, scoring, and reporting strategy (see #199).
 - The augmented Fastx format now permits annotation of 1 or more mate sequences (see #210).
+- Split `vcf.py` and `varmap.py` modules off from the `call.py` module (see #229).
 
 ### Fixed
 - Incorrect file names in the quick start documentation page (see 9f6bec06d4).
 - The `kevlar alac` procedure now accepts a stream of read partitions (instead of a stream of reads) at the Python API level, and correctly handles a single partition-labeled sequence file at the CLI level (see #165).
 - CIGARs that begin with I blocks (alternate allele contig is longer than reference locus) are now handled properly (see #191).
 - Bug with how `kevlar alac` handles "no reference match" scenarios resolved (see #192).
 - Bug with `kevlar count` when reading from multiple input files (see #202).
+- Can now call SNVs near INDELs (see #229).
 
 ## [0.3.0] - 2017-11-03
 

kevlar/__init__.py

@@ -29,6 +29,8 @@
 from kevlar import overlap
 from kevlar import sketch
 from kevlar import reference
+from kevlar import varmap
+from kevlar import vcf
 from kevlar.mutablestring import MutableString
 from kevlar.readgraph import ReadGraph
 from kevlar.seqio import parse_augmented_fastx, print_augmented_fastx