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path: root/bh20sequploader/qc_fasta.py
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2020-07-16Report similarity == 0Peter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-07minimap2 returns nothing when there is no alignment.Peter Amstutz
2020-07-07Use minimap2 instead of clustalw for fasta QCPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-03Add --skip-qc for faster batch importPeter Amstutz
2020-07-03Adding --skip-qcPeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-07-03Fix qc_fasta bug closing stream.Peter Amstutz
2020-06-22Better invalid sequence QC handlingPeter Amstutz
2020-06-22Handle upload & assembly of gzipped, paired-end fastqPeter Amstutz
2020-05-29Improved error output for the web uploaderPjotr Prins
2020-04-29Use subprocess invocation is backwards compatible with Python 3.5Peter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-28Call clustalw to compare sequence to referencePeter Amstutz
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-10Fix swapped fasta/fastqPeter Amstutz
Replace example sequence with COV19 reference instead of HIV. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
2020-04-10Add qc_fastaPeter Amstutz