Commit 0aaa1cbf authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 0.3.2

parent e526dae8

LICENSES.txt→LICENSE

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Copyright (c) 2016, Pacific Biosciences of California, Inc.

Copyright (c) 2016-2018, Pacific Biosciences of California, Inc.



All rights reserved.

MANIFEST.in

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include LICENSES.txt
 
include LICENSE

README.md

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pbalign maps PacBio reads to reference sequences.

<h1 align="center"><img src="http://www.pacb.com/wp-content/themes/pacific-biosciences/img/pacific-biosciences-logo-mobile.svg"/></h1>

<h1 align="center">pbalign</h1>

<p align="center">A python wrapper to easily align PacBio reads to reference sequences</p>



Want to know how to install and run pbalign?

***



## Availability

Latest version can be installed via bioconda package `pbalign`.



Please refer to our [official pbbioconda page](https://github.com/PacificBiosciences/pbbioconda)

for information on Installation, Support, License, Copyright, and Disclaimer.





## How To?

Want to know how to manually install or run pbalign?



Please refer to https://github.com/PacificBiosciences/pbalign/blob/master/doc/howto.rst

pbalign/__init__.py

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@@ -57,7 +57,7 @@ def get_changelist(): 
    return _get_changelist(_changelist)





VERSION = (0, 3, 1)

VERSION = (0, 4, 1)





def get_version():

pbalign/bampostservice.py

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@@ -37,7 +37,7 @@ 


# Author: Yuan Li



from __future__ import absolute_import

from __future__ import absolute_import, division, print_function

import logging

from pbalign.service import Service

from pbalign.utils.progutil import Execute
@@ -92,12 +92,13 @@ class BamPostService(Service): 
        except Exception:

            pass

        _stvmajor = int(_samtoolsversion[0])

        sort_nproc = max(1, nproc//4)

        if _stvmajor >= 1:

            cmd = 'samtools sort --threads {t} -m 4G -o {sortedBamFile} {unsortedBamFile}'.format(

                t=nproc, sortedBamFile=sortedBamFile, unsortedBamFile=unsortedBamFile)

            cmd = 'samtools sort --threads {t} -m 768M -o {sortedBamFile} {unsortedBamFile}'.format(

                t=sort_nproc, sortedBamFile=sortedBamFile, unsortedBamFile=unsortedBamFile)

        else:

            cmd = 'samtools sort --threads {t} -m 4G {unsortedBamFile} {prefix}'.format(

                t=nproc, unsortedBamFile=unsortedBamFile, prefix=sortedPrefix)

            cmd = 'samtools sort --threads {t} -m 768M {unsortedBamFile} {prefix}'.format(

                t=sort_nproc, unsortedBamFile=unsortedBamFile, prefix=sortedPrefix)

        Execute(self.name, cmd)



    def _makebai(self, sortedBamFile, outBaiFile):