Commit 7385d38e authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 0.8.0+git20181212.9fa8fc4+dfsg

parent 491db261

doc/index.rst

+11 −3
Original line number Diff line number Diff line
@@ -28,6 +28,14 @@ To install ``pbh5tools``, run the following command from the ``pbh5tools`` root 


   python setup.py install



If you do not have `root` or `sudo` permissions, you can install locally by:  



1. Installing pysam, numpy, Cython, and h5py to your home directory.  

              pip install --user --upgrade numpy h5py pysam cython

2. Running 

              python setup.py install --user





####################

Tool: bash5tools.py

####################
@@ -80,10 +88,10 @@ Usage 
Examples

--------



Extracting all Raw reads from ``input.bas.h5`` without any filtering

and exporting to FASTA (``myreads.fasta``): ::

Extracting all subreads reads from ``input.bas.h5`` without any filtering

and exporting to a FASTA file named ``myreads.fasta``: ::



    python bash5tools.py input.bas.h5 --outFilePrefix myreads --outType fasta --readType Raw

    python bash5tools.py --outFilePrefix myreads --outType fasta --readType subreads input.bas.h5



Extracting all CCS reads from ``input.bas.h5`` that have read lengths

larger than 100 and exporting to FASTQ (``myreads.fastq``): ::