--------------------- * Allow multiple inputs to readtagger * Allow passing multiple control files to confirm_insertions script * Fix matching of short 3p clipped sequences
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0.4.11
--------------------- * Add a script that merges findlcuster VCF output * Allow 5 nt overlaps at cluster consistency check * Include VALID_TSD in INFO field and write out PE support * Sort output VCF file * Generate IDs using reference_name start and cluster order * Improve support for arbitrary insertion names
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0.4.10
--------------------- * Include unmapped but tagged mates in veriefied tags * Update findcluster galaxy tool and fix softclip cluster ids * Use a unique ID as variant ID * Stop collection evidence once we reach 10000 reads * Speed up finding of soft clip clusters * Implement VCF output * Make loglevel configurable for findcluster script and add option to output log to file * Look for softclipped reads in a 15nt window and compare 5p clips by their end * Add script and tool to confirm/reject insertions * Refine the detection of TE clusters that are very close to each other * Verify that reads really support a specific insertion * Fix sorting to CRAM output * Move sorting of softclip clusters to merging phase * Skip finding softclipped clusters when skipping TE clusters * Annotate softclips as part of TEs * Embedd SoftClipClusterFinder in ClusterFinder * Fix softclipped positions when read contains deletions