.gitignore
.travis.yml
AUTHORS.rst
CONTRIBUTING.rst
HISTORY.rst
LICENCE
MANIFEST.in
README.rst
setup.py
tox.ini
docs/Makefile
docs/authors.rst
docs/conf.py
docs/contributing.rst
docs/history.rst
docs/index.rst
docs/installation.rst
docs/make.bat
docs/readme.rst
docs/usage.rst
idemux/__init__.py
idemux/__main__.py
idemux/_version.py
idemux/idemux.py
idemux.egg-info/PKG-INFO
idemux.egg-info/SOURCES.txt
idemux.egg-info/dependency_links.txt
idemux.egg-info/entry_points.txt
idemux.egg-info/not-zip-safe
idemux.egg-info/requires.txt
idemux.egg-info/top_level.txt
idemux/ioutils/__init__.py
idemux/ioutils/barcode.py
idemux/ioutils/file_handler.py
idemux/ioutils/parser.py
idemux/ioutils/writer.py
idemux/processing/__init__.py
idemux/processing/demuxer.py
idemux/resources/__init__.py
idemux/resources/barcodes/__init__.py
idemux/resources/barcodes/i1/__init__.py
idemux/resources/barcodes/i1/base_mapping_b384_l10.tsv
idemux/resources/barcodes/i1/base_mapping_b384_l12.tsv
idemux/resources/barcodes/i1/base_mapping_b96_l10.tsv
idemux/resources/barcodes/i1/base_mapping_b96_l12.tsv
idemux/resources/barcodes/i1/base_mapping_b96_l8.tsv
idemux/resources/barcodes/i5/__init__.py
idemux/resources/barcodes/i5/base_mapping_b384_l10.tsv
idemux/resources/barcodes/i5/base_mapping_b384_l12.tsv
idemux/resources/barcodes/i5/base_mapping_b96_l10.tsv
idemux/resources/barcodes/i5/base_mapping_b96_l12.tsv
idemux/resources/barcodes/i5/base_mapping_b96_l8.tsv
idemux/resources/barcodes/i5_rc/__init__.py
idemux/resources/barcodes/i5_rc/base_mapping_b384_l10.tsv
idemux/resources/barcodes/i5_rc/base_mapping_b384_l12.tsv
idemux/resources/barcodes/i5_rc/base_mapping_b96_l10.tsv
idemux/resources/barcodes/i5_rc/base_mapping_b96_l12.tsv
idemux/resources/barcodes/i5_rc/base_mapping_b96_l8.tsv
idemux/resources/barcodes/i7/__init__.py
idemux/resources/barcodes/i7/base_mapping_b384_l10.tsv
idemux/resources/barcodes/i7/base_mapping_b384_l12.tsv
idemux/resources/barcodes/i7/base_mapping_b96_l10.tsv
idemux/resources/barcodes/i7/base_mapping_b96_l12.tsv
idemux/resources/barcodes/i7/base_mapping_b96_l8.tsv
tests/__init__.py
tests/test_barcode.py
tests/test_demuxer.py
tests/test_idemux.py
tests/test_parser.py
tests/resources/end_to_end/i1_read_1.fastq.gz
tests/resources/end_to_end/i1_read_2.fastq.gz
tests/resources/end_to_end/i1_sample_sheet.csv
tests/resources/end_to_end/i5_i1_read_1.fastq.gz
tests/resources/end_to_end/i5_i1_read_2.fastq.gz
tests/resources/end_to_end/i5_i1_sample_sheet.csv
tests/resources/end_to_end/i7_i1_read_1.fastq.gz
tests/resources/end_to_end/i7_i1_read_2.fastq.gz
tests/resources/end_to_end/i7_i1_sample_sheet.csv
tests/resources/end_to_end/i7_i5_i1_read_1.fastq.gz
tests/resources/end_to_end/i7_i5_i1_read_2.fastq.gz
tests/resources/end_to_end/i7_i5_i1_sample_sheet.csv
tests/resources/end_to_end/i7_i5_read_1.fastq.gz
tests/resources/end_to_end/i7_i5_read_2.fastq.gz
tests/resources/end_to_end/i7_i5_sample_sheet.csv
tests/resources/fastq/i5_i1_read_1.fastq.gz
tests/resources/fastq/i5_i1_read_2.fastq.gz
tests/resources/fastq/i7+2_i5_i1_read_1.fastq.gz
tests/resources/fastq/i7+2_i5_i1_read_2.fastq.gz
tests/resources/fastq/i7-2_i5_i1_read_1.fastq.gz
tests/resources/fastq/i7-2_i5_i1_read_2.fastq.gz
tests/resources/fastq/i7_i1_read_1.fastq.gz
tests/resources/fastq/i7_i1_read_2.fastq.gz
tests/resources/fastq/i7_i5+2_i1_read_1.fastq.gz
tests/resources/fastq/i7_i5+2_i1_read_2.fastq.gz
tests/resources/fastq/i7_i5_i1_read_1.fastq.gz
tests/resources/fastq/i7_i5_i1_read_2.fastq.gz
tests/resources/fastq/i7_i5_noi1_read_1.fastq.gz
tests/resources/fastq/i7_i5_noi1_read_2.fastq.gz
tests/resources/sample_sheet/fail/column_missing.csv
tests/resources/sample_sheet/fail/duplicate_barcodes.csv
tests/resources/sample_sheet/fail/duplicate_sample.csv
tests/resources/sample_sheet/fail/i7all_i5some_i1_all.csv
tests/resources/sample_sheet/fail/i7none_i5some_i1some.csv
tests/resources/sample_sheet/fail/i7some_i5all_i1all.csv
tests/resources/sample_sheet/fail/missing_comma.csv
tests/resources/sample_sheet/fail/no_barcodes.csv
tests/resources/sample_sheet/fail/wrong_header.csv
tests/resources/sample_sheet/pass/i7all_i5all_i1all.csv
tests/resources/sample_sheet/pass/i7all_i5all_i1none.csv
tests/resources/sample_sheet/pass/i7all_i5all_i1some.csv
tests/resources/sample_sheet/pass/i7all_i5no_i1some.csv
tests/resources/sample_sheet/pass/i7all_i5none_i1none.csv
tests/resources/sample_sheet/pass/i7none_i5all_i1all.csv
tests/resources/sample_sheet/pass/i7none_i5all_i1none.csv
tests/resources/sample_sheet/pass/i7none_i5all_i1some.csv
tests/resources/sample_sheet/pass/i7none_i5none_i1all.csv