[med-svn] [Git][med-team/pbh5tools][upstream] New upstream version 0.8.0+git20181212.9fa8fc4+dfsg

[Andreas Tille]

Andreas Tille pushed to branch upstream at Debian Med / pbh5tools


Commits:
7385d38e by Andreas Tille at 2019-12-07T08:10:00Z
New upstream version 0.8.0+git20181212.9fa8fc4+dfsg
- - - - -


1 changed file:

- doc/index.rst


Changes:

=====================================
doc/index.rst
=====================================
@@ -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``): ::



View it on GitLab: https://salsa.debian.org/med-team/pbh5tools/commit/7385d38eff8bb426d02e5718b46004192f0fe164

-- 
View it on GitLab: https://salsa.debian.org/med-team/pbh5tools/commit/7385d38eff8bb426d02e5718b46004192f0fe164
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