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update readme
author Daniel Blankenberg <dan@bx.psu.edu>
date Tue, 27 Aug 2013 14:54:49 -0400
parents 66a4325d9394
children
files README.rst tools/naive_variant_detector.xml
diffstat 2 files changed, 44 insertions(+), 44 deletions(-) [+]
line wrap: on
line diff
--- a/README.rst	Tue Aug 27 14:37:12 2013 -0400
+++ b/README.rst	Tue Aug 27 14:54:49 2013 -0400
@@ -23,60 +23,60 @@
 The output is in VCF format.
 
 Example VCF output line, without reporting by strand:
- ``chrM	16029	.	T	G,A,C	.	.	AC=15,9,5;AF=0.00155311658729,0.000931869952371,0.000517705529095	GT:AC:AF:NC	0/0:15,9,5:0.00155311658729,0.000931869952371,0.000517705529095:A=9,C=5,T=9629,G=15,``
+    ``chrM	16029	.	T	G,A,C	.	.	AC=15,9,5;AF=0.00155311658729,0.000931869952371,0.000517705529095	GT:AC:AF:NC	0/0:15,9,5:0.00155311658729,0.000931869952371,0.000517705529095:A=9,C=5,T=9629,G=15,``
 
 Example VCF output line, when reporting by strand:
- ``chrM	16029	.	T	G,A,C	.	.	AC=15,9,5;AF=0.00155311658729,0.000931869952371,0.000517705529095	GT:AC:AF:NC	0/0:15,9,5:0.00155311658729,0.000931869952371,0.000517705529095:+T=3972,-A=9,-C=5,-T=5657,-G=15,``
+    ``chrM	16029	.	T	G,A,C	.	.	AC=15,9,5;AF=0.00155311658729,0.000931869952371,0.000517705529095	GT:AC:AF:NC	0/0:15,9,5:0.00155311658729,0.000931869952371,0.000517705529095:+T=3972,-A=9,-C=5,-T=5657,-G=15,``
 
 **Options**
 
 Reference Genome:
 
-  Ensure that you have selected the correct reference genome, either from the list of built-in genomes or by selecting the corresponding FASTA file from your history.
+    Ensure that you have selected the correct reference genome, either from the list of built-in genomes or by selecting the corresponding FASTA file from your history.
 
 Restrict to regions:
 
- You can specify any number of regions on which you would like to receive results. You can specify just a chromosome name, or a chromosome name and start postion, or a chromosome name and start and end position for the set of desired regions. 
+    You can specify any number of regions on which you would like to receive results. You can specify just a chromosome name, or a chromosome name and start postion, or a chromosome name and start and end position for the set of desired regions. 
 
 Minimum number of reads needed to consider a REF/ALT:
 
- This value declares the minimum number of reads containing a particular base at each position in order to list and use said allele in genotyping calls. Default is 0.
+    This value declares the minimum number of reads containing a particular base at each position in order to list and use said allele in genotyping calls. Default is 0.
 
 Minimum base quality:
 
- The minimum base quality score needed for the position in a read to be used for nucleotide counts and genotyping. Default is no filter.
+    The minimum base quality score needed for the position in a read to be used for nucleotide counts and genotyping. Default is no filter.
 
 Minimum mapping quality:
 
- The minimum mapping quality score needed to consider a read for nucleotide counts and genotyping. Default is no filter.
+    The minimum mapping quality score needed to consider a read for nucleotide counts and genotyping. Default is no filter.
 
 Ploidy:
 
- The number of genotype calls to make at each reported position.
+    The number of genotype calls to make at each reported position.
 
 Only write out positions with with possible alternate alleles:
 
- When set, only positions which have at least one non-reference nucleotide which passes declare filters will be present in the output.
+    When set, only positions which have at least one non-reference nucleotide which passes declare filters will be present in the output.
 
 Report counts by strand:
 
- When set, nucleotide counts (NC) will be reported in reference to the aligned read's source strand. Reported as: <strand><BASE>=<COUNT>.
+    When set, nucleotide counts (NC) will be reported in reference to the aligned read's source strand. Reported as: <strand><BASE>=<COUNT>.
 
 Choose the dtype to use for storing coverage information:
 
- This controls the maximum depth value for each nucleotide/position/strand (when specified). Smaller values require the least amount of memory, but have smaller maximal limits.
+    This controls the maximum depth value for each nucleotide/position/strand (when specified). Smaller values require the least amount of memory, but have smaller maximal limits.
  
- +--------+----------------------------+
- | name   | maximum coverage value     |
- +========+============================+
- | uint8  | 255                        |
- +--------+----------------------------+
- | uint16 | 65,535                     |
- +--------+----------------------------+
- | uint32 | 4,294,967,295              |
- +--------+----------------------------+
- | uint64 | 18,446,744,073,709,551,615 |
- +--------+----------------------------+
+        +--------+----------------------------+
+        | name   | maximum coverage value     |
+        +========+============================+
+        | uint8  | 255                        |
+        +--------+----------------------------+
+        | uint16 | 65,535                     |
+        +--------+----------------------------+
+        | uint32 | 4,294,967,295              |
+        +--------+----------------------------+
+        | uint64 | 18,446,744,073,709,551,615 |
+        +--------+----------------------------+
 
 
 ------
--- a/tools/naive_variant_detector.xml	Tue Aug 27 14:37:12 2013 -0400
+++ b/tools/naive_variant_detector.xml	Tue Aug 27 14:54:49 2013 -0400
@@ -126,60 +126,60 @@
 The output is in VCF format.
 
 Example VCF output line, without reporting by strand:
- ``chrM	16029	.	T	G,A,C	.	.	AC=15,9,5;AF=0.00155311658729,0.000931869952371,0.000517705529095	GT:AC:AF:NC	0/0:15,9,5:0.00155311658729,0.000931869952371,0.000517705529095:A=9,C=5,T=9629,G=15,``
+    ``chrM	16029	.	T	G,A,C	.	.	AC=15,9,5;AF=0.00155311658729,0.000931869952371,0.000517705529095	GT:AC:AF:NC	0/0:15,9,5:0.00155311658729,0.000931869952371,0.000517705529095:A=9,C=5,T=9629,G=15,``
 
 Example VCF output line, when reporting by strand:
- ``chrM	16029	.	T	G,A,C	.	.	AC=15,9,5;AF=0.00155311658729,0.000931869952371,0.000517705529095	GT:AC:AF:NC	0/0:15,9,5:0.00155311658729,0.000931869952371,0.000517705529095:+T=3972,-A=9,-C=5,-T=5657,-G=15,``
+    ``chrM	16029	.	T	G,A,C	.	.	AC=15,9,5;AF=0.00155311658729,0.000931869952371,0.000517705529095	GT:AC:AF:NC	0/0:15,9,5:0.00155311658729,0.000931869952371,0.000517705529095:+T=3972,-A=9,-C=5,-T=5657,-G=15,``
 
 **Options**
 
 Reference Genome:
 
-  Ensure that you have selected the correct reference genome, either from the list of built-in genomes or by selecting the corresponding FASTA file from your history.
+    Ensure that you have selected the correct reference genome, either from the list of built-in genomes or by selecting the corresponding FASTA file from your history.
 
 Restrict to regions:
 
- You can specify any number of regions on which you would like to receive results. You can specify just a chromosome name, or a chromosome name and start postion, or a chromosome name and start and end position for the set of desired regions. 
+    You can specify any number of regions on which you would like to receive results. You can specify just a chromosome name, or a chromosome name and start postion, or a chromosome name and start and end position for the set of desired regions. 
 
 Minimum number of reads needed to consider a REF/ALT:
 
- This value declares the minimum number of reads containing a particular base at each position in order to list and use said allele in genotyping calls. Default is 0.
+    This value declares the minimum number of reads containing a particular base at each position in order to list and use said allele in genotyping calls. Default is 0.
 
 Minimum base quality:
 
- The minimum base quality score needed for the position in a read to be used for nucleotide counts and genotyping. Default is no filter.
+    The minimum base quality score needed for the position in a read to be used for nucleotide counts and genotyping. Default is no filter.
 
 Minimum mapping quality:
 
- The minimum mapping quality score needed to consider a read for nucleotide counts and genotyping. Default is no filter.
+    The minimum mapping quality score needed to consider a read for nucleotide counts and genotyping. Default is no filter.
 
 Ploidy:
 
- The number of genotype calls to make at each reported position.
+    The number of genotype calls to make at each reported position.
 
 Only write out positions with with possible alternate alleles:
 
- When set, only positions which have at least one non-reference nucleotide which passes declare filters will be present in the output.
+    When set, only positions which have at least one non-reference nucleotide which passes declare filters will be present in the output.
 
 Report counts by strand:
 
- When set, nucleotide counts (NC) will be reported in reference to the aligned read's source strand. Reported as: &lt;strand&gt;&lt;BASE&gt;=&lt;COUNT&gt;.
+    When set, nucleotide counts (NC) will be reported in reference to the aligned read's source strand. Reported as: &lt;strand&gt;&lt;BASE&gt;=&lt;COUNT&gt;.
 
 Choose the dtype to use for storing coverage information:
 
- This controls the maximum depth value for each nucleotide/position/strand (when specified). Smaller values require the least amount of memory, but have smaller maximal limits.
+    This controls the maximum depth value for each nucleotide/position/strand (when specified). Smaller values require the least amount of memory, but have smaller maximal limits.
 
- +--------+----------------------------+
- | name   | maximum coverage value     |
- +========+============================+
- | uint8  | 255                        |
- +--------+----------------------------+
- | uint16 | 65,535                     |
- +--------+----------------------------+
- | uint32 | 4,294,967,295              |
- +--------+----------------------------+
- | uint64 | 18,446,744,073,709,551,615 |
- +--------+----------------------------+
+        +--------+----------------------------+
+        | name   | maximum coverage value     |
+        +========+============================+
+        | uint8  | 255                        |
+        +--------+----------------------------+
+        | uint16 | 65,535                     |
+        +--------+----------------------------+
+        | uint32 | 4,294,967,295              |
+        +--------+----------------------------+
+        | uint64 | 18,446,744,073,709,551,615 |
+        +--------+----------------------------+
 
 ------