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Update index.rst
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susannasiebert committed Nov 8, 2016
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Expand Up @@ -26,7 +26,7 @@ pVAC-Seq now supports local installs of IEDB MHC `class I <http://tools.iedb.org

This version adds a new column ``Mutation Position`` to the report output. This column denotes the 1-based start position of the mutation in the ``MT Epitope Seq``. If the value is ``0`` the mutation start position is before the first position in the epitope.

pVAC-Seq now allows the user to specify the number of retries after a request to the IEDB RESTful interface fails. The number of retries can be set by using the ``--iedb-retries`` parameter. Previously this number was hard-coded to 3. More retries might be necessary in order to get a successful response for complex queries (e.g., large number of variants, long frameshift downstream sequences, choice of compute-intensive prediction algorithms). This parameter should be used in conjunction with ``--fasta-size`` and ``--downstream-sequence-length`` for the hightest likelihood of sucess of finishing a pVAC-Seq run.
pVAC-Seq now allows the user to specify the number of retries after a request to the IEDB RESTful interface fails. The number of retries can be set by using the ``--iedb-retries`` parameter. Previously this number was hard-coded to 3. More retries might be necessary in order to get a successful response for complex queries (e.g., large number of variants, long frameshift downstream sequences, choice of compute-intensive prediction algorithms). This parameter should be used in conjunction with ``--fasta-size`` and ``--downstream-sequence-length`` for the highest likelihood of success of finishing a pVAC-Seq run.

This release fixes an error that was introduced in the previous version which would occur when the user would try to rerun a process in the same output directory.

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