Recent changes to qProfiler

qProfiler modified by John Pearson

John Pearson — Tue, 18 Jul 2017 06:19:35 -0000

--- v11
+++ v12
@@ -3,8 +3,6 @@
 While the XML file is useful for extracting values for further analysis, a visual representation of the data is more useful in most cases so another tool (qvisualise) was created to parse the qprofiler XML files and produce HTML output with embedded graphs.

 qProfiler uses the [Picard](https://sourceforge.net/apps/mediawiki/picard/index.php?title=Main_Page) library to access BAM files.
-
-[qprofiler 2.0]

 System Requirements
 -------------------

qProfiler modified by John Pearson

John Pearson — Tue, 18 Jul 2017 06:16:52 -0000

--- v10
+++ v11
@@ -4,7 +4,7 @@

 qProfiler uses the [Picard](https://sourceforge.net/apps/mediawiki/picard/index.php?title=Main_Page) library to access BAM files.

-[qprofiler tmp]
+[qprofiler 2.0]

 System Requirements
 -------------------

qProfiler modified by John Pearson

John Pearson — Tue, 18 Jul 2017 06:11:47 -0000

--- v9
+++ v10
@@ -4,7 +4,7 @@

 qProfiler uses the [Picard](https://sourceforge.net/apps/mediawiki/picard/index.php?title=Main_Page) library to access BAM files.

-[qprofiler 2.0]
+[qprofiler tmp]

 System Requirements
 -------------------

qProfiler modified by John Pearson

John Pearson — Tue, 18 Jul 2017 06:01:41 -0000

--- v8
+++ v9
@@ -4,6 +4,7 @@

 qProfiler uses the [Picard](https://sourceforge.net/apps/mediawiki/picard/index.php?title=Main_Page) library to access BAM files.

+[qprofiler 2.0]

 System Requirements
 -------------------

qProfiler modified by Ollie Holmes

Ollie Holmes — Wed, 09 Apr 2014 02:18:47 -0000

--- v7
+++ v8
@@ -15,7 +15,7 @@
 Installation
 ------------

-* Download the [qprofiler tar file(http://sourceforge.net/projects/adamajava/files/qprofiler.tar.bz2/download)
+* Download the [qprofiler tar file](http://sourceforge.net/projects/adamajava/files/qprofiler.tar.bz2/download)
 * Untar the tar file into a directory of your choice

 You should see something like this:

qProfiler modified by John Pearson

John Pearson — Thu, 03 Apr 2014 11:55:53 -0000

--- v6
+++ v7
@@ -1,4 +1,4 @@
-profiler is a standalone Java app that takes in BAM or FASTQ files and provides an XML file containing basic summary statistics for each file. If no output file is specified (a supplied file with a .xml extension is considered an output file), then the process will write to a default file (currently qprofiler.xml).
+qprofiler is a standalone Java app that takes in BAM or FASTQ files and provides an XML file containing basic summary statistics for each file. If no output file is specified (a supplied file with a .xml extension is considered an output file), then the process will write to a default file (currently qprofiler.xml).

 While the XML file is useful for extracting values for further analysis, a visual representation of the data is more useful in most cases so another tool (qvisualise) was created to parse the qprofiler XML files and produce HTML output with embedded graphs.

qProfiler modified by John Pearson

John Pearson — Thu, 03 Apr 2014 11:55:32 -0000

--- v5
+++ v6
@@ -16,8 +16,9 @@
 ------------

 * Download the [qprofiler tar file(http://sourceforge.net/projects/adamajava/files/qprofiler.tar.bz2/download)
-* Untar the tar file into a directory of your choice.
+* Untar the tar file into a directory of your choice

+You should see something like this:

 ~~~~
 [oholmes@minion0 test_adama_tools_data]$ tar xjvf qprofiler.tar.bz2
@@ -57,4 +58,4 @@
      -ntP 4 -ntC 16
 ~~~~

-NOTE that BWA mapped bam files need to be run with the additional parameter -validation SILENT otherwise Picard will throw an exception.
+NOTE that BWA mapped bam files may need to be run with the optional parameter -validation SILENT otherwise Picard will throw an exception.

qProfiler modified by John Pearson

John Pearson — Thu, 03 Apr 2014 11:49:37 -0000

--- v4
+++ v5
@@ -1,46 +1,60 @@
-qProfiler
-=========
-Stand alone Java app that takes in a number of files as arguments, and provides an XML file containing basic summary statistics for each file. If no output file is specified (a supplied file with a .xml extension is considered an output file), then the process will write to a default file (currently qprofiler.xml). While the XML file is useful for extracting values for further analysis, a visual representation of the data is more useful in most cases so another tool (qvisualise) was created to parse the qprofiler XML files and produce HTML output with embedded graphs.
-The primary use for qProfiler is to characterise BAM files.
-qProfiler uses the picard libraries to access BAM files.
+profiler is a standalone Java app that takes in BAM or FASTQ files and provides an XML file containing basic summary statistics for each file. If no output file is specified (a supplied file with a .xml extension is considered an output file), then the process will write to a default file (currently qprofiler.xml).
+
+While the XML file is useful for extracting values for further analysis, a visual representation of the data is more useful in most cases so another tool (qvisualise) was created to parse the qprofiler XML files and produce HTML output with embedded graphs. 
+
+qProfiler uses the [Picard](https://sourceforge.net/apps/mediawiki/picard/index.php?title=Main_Page) library to access BAM files.

 System Requirements
-=====
-Java 1.7
-Multi-core machine (ideally) and 12GB of RAM
+-------------------
+
+* Java 1.7
+* Multi-core machine (ideally) and 12GB of RAM
+

 Installation
-===========
-Download the [qprofiler tar file](http://sourceforge.net/projects/adamajava/files/qprofiler.tar.bz2/download)
-Untar the tar file into a directory of your choice.
+------------

-    [oholmes@minion0 test_adama_tools_data]$ tar xjvf qprofiler.tar.bz2
-    jopt-simple-3.2.jar
-    picard-1.110.jar
-    qcommon-0.1pre.jar
-    qio-0.1pre.jar
-    qmule-0.1pre.jar
-    qpicard-0.1pre.jar
-    qprofiler-1.0.jar
-    qvisualise-0.1pre.jar
-    sam-1.110.jar
-    [oholmes@minion0 test_adama_tools_data]$
+* Download the [qprofiler tar file(http://sourceforge.net/projects/adamajava/files/qprofiler.tar.bz2/download)
+* Untar the tar file into a directory of your choice.
+
+
+~~~~
+[oholmes@minion0 test_adama_tools_data]$ tar xjvf qprofiler.tar.bz2
+jopt-simple-3.2.jar
+picard-1.110.jar
+qcommon-0.1pre.jar
+qio-0.1pre.jar
+qmule-0.1pre.jar
+qpicard-0.1pre.jar
+qprofiler-1.0.jar
+qvisualise-0.1pre.jar
+sam-1.110.jar
+[oholmes@minion0 test_adama_tools_data]$
+~~~~

 Usage
-==
-    java -jar qprofiler-1.0.jar 
-    -input     
-    -output 
-    -log 
-    -ntC  OPTIONAL
-    -ntP  OPTIONAL
-    -validation Possible values: {STRICT, LENIENT, SILENT}
+-----

+~~~~
+java -jar qprofiler-1.0.jar 
+     -input     
+     -output 
+     -log 
+     -ntC  OPTIONAL
+     -ntP  OPTIONAL
+     -validation Possible values: {STRICT, LENIENT, SILENT}
+~~~~

 For example, to run on a 16 core node:

-    java -jar qprofiler-1.0.jar -input /sample_virus.BWA-backtrack.bam -log /sample_virus.BWA-backtrack.bam.qp.log -output /sample_virus.BWA-backtrack.bam.qp.xml -ntP 4 -ntC 16
+~~~~
+java -jar qprofiler-1.0.jar \
+     -input /sample_virus.BWA-backtrack.bam \
+     -log /sample_virus.BWA-backtrack.bam.qp.log \
+     -output /sample_virus.BWA-backtrack.bam.qp.xml \
+     -ntP 4 -ntC 16
+~~~~

-NOTE that BWA mapped bam files need to be run with -validation SILENT otherwise picard will throw an exception.
+NOTE that BWA mapped bam files need to be run with the additional parameter -validation SILENT otherwise Picard will throw an exception.

qProfiler modified by Ollie Holmes

Ollie Holmes — Thu, 03 Apr 2014 04:52:58 -0000

--- v3
+++ v4
@@ -36,7 +36,7 @@
     -log 
     -ntC  OPTIONAL
     -ntP  OPTIONAL
-    -validation

qProfiler modified by Ollie Holmes

Ollie Holmes — Thu, 03 Apr 2014 04:37:51 -0000

--- v2
+++ v3
@@ -12,7 +12,7 @@

 Installation
 ===========
-Download the qprofiler tar file.
+Download the [qprofiler tar file](http://sourceforge.net/projects/adamajava/files/qprofiler.tar.bz2/download)
 Untar the tar file into a directory of your choice.

     [oholmes@minion0 test_adama_tools_data]$ tar xjvf qprofiler.tar.bz2