DEVELOPMENT.rst
HISTORY.rst
MANIFEST.in
README.rst
ROADMAP.rst
setup.py
readtagger/__init__.py
readtagger/allow_dovetailing.py
readtagger/bam_io.py
readtagger/bwa.py
readtagger/cap3.py
readtagger/cigar.py
readtagger/cluster.py
readtagger/fasta_io.py
readtagger/findcluster.py
readtagger/genotype.py
readtagger/gff_io.py
readtagger/mateoperations.py
readtagger/readtagger.py
readtagger/tag_softclip.py
readtagger/tagcluster.py
readtagger/tags.py
readtagger/targetsiteduplication.py
readtagger/update_mapq.py
readtagger/verify.py
readtagger/write_supplementary_fastq.py
readtagger.egg-info/PKG-INFO
readtagger.egg-info/SOURCES.txt
readtagger.egg-info/dependency_links.txt
readtagger.egg-info/entry_points.txt
readtagger.egg-info/requires.txt
readtagger.egg-info/top_level.txt
readtagger/cli/__init__.py
readtagger/cli/add_matesequence.py
readtagger/cli/annotate_softclipped_reads.py
readtagger/cli/findcluster.py
readtagger/cli/readtagger_cli.py
readtagger/cli/update_mapq.py
readtagger/cli/write_supplementary_fastq.py
test/test_cluster.py
test/test_clusterfinder.py
test/test_dovetailing.py
test/test_io.py
test/test_mateoperations.py
test/test_readtagger.py
test/test_tag_softclip.py
test/test_tagcluster.py
test/test_update_mapq.py
test/test_verify.py
test/test_write_supplementary.py