Recent changes to qBamfilter

qBamfilter modified by John Pearson

John Pearson — Sun, 29 May 2016 23:13:49 -0000

--- v9
+++ v10
@@ -6,7 +6,7 @@

 qbamfilter requires java 7 and (ideally) a multi-core machine, although it operates in single-threaded mode by default.  You can tune the amount of memory used by qbamfilter by specifying the number of records to store in memory (--maxRecordNumber).  You can also opt to sort the output BAM and the BAM will be automatically indexed if the sort-by-coordinate option is specified.

-* Download the [qfamfilter tar file](http://sourceforge.net/projects/adamajava/files/qbamfilter.tar/download)
+* Download the [qbamfilter tar file](http://sourceforge.net/projects/adamajava/files/qbamfilter.tar/download)
 * Untar the tar file into a directory of your choice
 * current version is 1.1pre.

qBamfilter modified by John Pearson

John Pearson — Mon, 26 May 2014 05:51:04 -0000

--- v8
+++ v9
@@ -1,10 +1,10 @@
 [TOC]
 #Introduction#
-qbamfilter - select reads from a BAM files based on a user-supplied query.  qbamfilter is available as a standalone application and is incorporated into the majority of AdamaJava tools as an input filter.  Reads that match the query are written to a new BAM file and reads that do not are dropped or optionally written to a different BAM file.
+qbamfilter - select reads from a BAM files based on a user-supplied query.  qbamfilter is available as a standalone application and is incorporated into the majority of AdamaJava tools as a library to provide filtering of BAM records.  For the standalone application, reads that match the query are written to a new BAM file and reads that do not are dropped or optionally written to a different BAM file.  For the library use-case, only BAM records that pass the query string are accepted for further processing by the AdamaJava tool.

 #Installation#

-qbamfilter requires java 7 and (ideally) a multi-core machine, although it operates in single-threaded mode by default.  You can tune the amount of memory used by qbamfilter by specifying the number of records to store in memory.  You can also opt to sort the output BAM and the BAM will be automatically indexed if the sort-by-coordinate option is specified.
+qbamfilter requires java 7 and (ideally) a multi-core machine, although it operates in single-threaded mode by default.  You can tune the amount of memory used by qbamfilter by specifying the number of records to store in memory (--maxRecordNumber).  You can also opt to sort the output BAM and the BAM will be automatically indexed if the sort-by-coordinate option is specified.

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

qBamfilter modified by John Pearson

John Pearson — Mon, 26 May 2014 05:48:03 -0000

--- v7
+++ v8
@@ -60,15 +60,20 @@
 The -q option is the heart of qbamfilter as it defines the actual filter to be applied. Use of this option is also continually in flux as expansion of the functionality of the filtering code is the focus of most ongoing development of this tool. The current query usage is of the form:

 ~~~~
-"operator ( condition, condition*, query* )" 
+operator( condition, condition*, query* )
 ~~~~

-i.e., it lists one or more conditions joined by operators. Currently there are only two operators available - and and or. You can also insert query language as condition into the final query string. For example:
+i.e., it lists one or more conditions joined by operators. Currently there are only two operators available - and() and or().  A more complicated example is shown here:

 ~~~~
-" and (Cigar_M > 35, RNAME =~ chr*, or (MAPQ > 50, option_ZM == 1), Flag_DuplicateRead == false )"
+and( Cigar_M > 35,
+     RNAME =~ chr*,
+     or( MAPQ > 50, option_ZM == 1 ),
+     Flag_DuplicateRead == false )
 ~~~~

-This query string, joined by operator and and contains three conditions. here we treat the sub query or (MAPQ > 50, option_ZM == 1) as one condition.
+This query string shows an and() operator with 4 conditions, one of which is an example of the use of the or() operator.  This query has the effect of only allowing through BAM records where there are 35 or more bases with an "M" CIGAR designation, and where the sequence matched starts with the string 'chr', and where the mapping quality is greater than 50 or the ZM option is set to 1, and where the read is not a duplicate.

-Please [click here](/p/adamajava/wiki/qbamfilter_query/) for further information including example and detailed explaination
+It is important to remember that the query must evaluate to 'true" for the read to be passed by the query and therefore to be written to the --output BAM file.
+
+Please [click here](/p/adamajava/wiki/qbamfilter_query/) for examples and a more detailed explanation of the qbamfilter query language.

qBamfilter modified by John Pearson

John Pearson — Mon, 26 May 2014 05:39:35 -0000

--- v6
+++ v7
@@ -1,18 +1,16 @@
 [TOC]
 #Introduction#
-qbamfilter - reporting all satisfied BAM/SAM record based on a query from input SAM/BAM file to output BAM file. It is optional to report unsatisfied records to specified output BAM
+qbamfilter - select reads from a BAM files based on a user-supplied query.  qbamfilter is available as a standalone application and is incorporated into the majority of AdamaJava tools as an input filter.  Reads that match the query are written to a new BAM file and reads that do not are dropped or optionally written to a different BAM file.

 #Installation#

-qbamfilter requires java 7 and (ideally) a multi-core machine (single threads by default). qbamfilter is memory adjustable: You can specify the number of records to store on RAM. It is also designed for fast query execution by specify the number of threads. You can also specify the order method to sort the output BAMs, it creates index file if the output BAM is sorted by coordinate.
-
- 
+qbamfilter requires java 7 and (ideally) a multi-core machine, although it operates in single-threaded mode by default.  You can tune the amount of memory used by qbamfilter by specifying the number of records to store in memory.  You can also opt to sort the output BAM and the BAM will be automatically indexed if the sort-by-coordinate option is specified.

 * Download the [qfamfilter tar file](http://sourceforge.net/projects/adamajava/files/qbamfilter.tar/download)
 * Untar the tar file into a directory of your choice
 * current version is 1.1pre.

-You should see jar files for qsnp and its dependencies:
+You should see jar files for qbamfilter and its dependencies:

 ~~~~
 >tar xjvf qfamfilter.tar 
@@ -29,32 +27,33 @@
 #Usage#

 ~~~~
-java -jar bamfilter-1.1pre.jar  -q "[query]" -o  -i   --log  [options]
+java -jar bamfilter-1.1pre.jar -i  -q "[query]" -o  --log  [options]

 Option                                  Description                            
 ------                                  -----------   
 -h, --help                              Shows this help message.     
 -v, --version                           Print version info.      
--i, --input                      A SAM/BAM file with full path 
--o, --output                    A full path BAM file storing all satisfied SAM records    
--q, --query                      A string simulated from sql query. All reads satisfied 
-                                        by this query will be report to output file.   
---log                                   It is compulsory to list you log file with full path here  
---loglevel                              (Optional)  Logging level required, e.g. INFO, DEBUG. 
+-i, --input                   A SAM/BAM file with full path 
+-o, --output                 A full path BAM file storing all satisfied SAM records    
+-q, --query                      Query string. All reads satisfying this query will be written 
+                                        to the output file.   
+    --log                      A log file must be specified
+    --loglevel                          (Optional)  Logging level required, e.g. INFO, DEBUG. 
                                         If no parameter is specified, will default to INFO                          
--f, --filterOut              (Optional) a full path BAM file storing all unsatisfied SAM 
-                                        records. Without this option, all unmatched reads will be discarded.             
+-f, --filterOut              (Optional) BAM file to hold records that did not satisfy
+                                        the query. Without this option, all unmatched reads will
+                                        be discarded.             
 -m, --maxRecordNumber  (Optional) RAM queue size of BAM records during reading and 
                                         outputting, unit K (eg, 1 equal 1,000 records). default unit will 
                                         be 100,  that is maximum 100,000 reads.              
---sort                                  (Optional) specify sort order here [queryname,coordinate,unsorted],     
-                                        here we use unsorted as default.     
+    --sort                              (Optional) sort order: queryname, coordinate, unsorted (default) 
 -t, --threadNumber        (Optional) the number of filtering thread is allowed 
                                         during process. Default number will be 1.            
---tmpdir                                (Optional) the location of temporary BAMs will created. 
+    --tmpdir                            (Optional) the location of temporary BAMs will created. 
                                         Default location will depend on picard behaviors      
---validation                            (Optional)  How strict to read a SAM or BAM. Possible values: 
-                                        {STRICT, LENIENT, SILENT}. Without this option, "LENIENT" will be set.        
+    --validation                        (Optional)  How strict to read a SAM or BAM. Possible values: 
+                                        {STRICT, LENIENT, SILENT}. Without this option, "LENIENT" will
+                                        be set.        
 ~~~~

 #query language#

qBamfilter modified by q.xu

q.xu — Fri, 23 May 2014 05:41:27 -0000

--- v5
+++ v6
@@ -67,7 +67,9 @@
 i.e., it lists one or more conditions joined by operators. Currently there are only two operators available - and and or. You can also insert query language as condition into the final query string. For example:

 ~~~~
-" and (Cigar_M > 35, or (MAPQ > 50, option_ZM == 1), Flag_DuplicateRead == false)"
+" and (Cigar_M > 35, RNAME =~ chr*, or (MAPQ > 50, option_ZM == 1), Flag_DuplicateRead == false )"
 ~~~~

 This query string, joined by operator and and contains three conditions. here we treat the sub query or (MAPQ > 50, option_ZM == 1) as one condition.
+
+Please [click here](/p/adamajava/wiki/qbamfilter_query/) for further information including example and detailed explaination

qBamfilter modified by q.xu

q.xu — Fri, 23 May 2014 05:38:25 -0000

--- v4
+++ v5
@@ -56,3 +56,18 @@
 --validation                            (Optional)  How strict to read a SAM or BAM. Possible values: 
                                         {STRICT, LENIENT, SILENT}. Without this option, "LENIENT" will be set.        
 ~~~~
+
+#query language#
+The -q option is the heart of qbamfilter as it defines the actual filter to be applied. Use of this option is also continually in flux as expansion of the functionality of the filtering code is the focus of most ongoing development of this tool. The current query usage is of the form:
+
+~~~~
+"operator ( condition, condition*, query* )" 
+~~~~
+
+i.e., it lists one or more conditions joined by operators. Currently there are only two operators available - and and or. You can also insert query language as condition into the final query string. For example:
+
+~~~~
+" and (Cigar_M > 35, or (MAPQ > 50, option_ZM == 1), Flag_DuplicateRead == false)"
+~~~~
+
+This query string, joined by operator and and contains three conditions. here we treat the sub query or (MAPQ > 50, option_ZM == 1) as one condition.

qBamfilter modified by q.xu

q.xu — Fri, 23 May 2014 05:33:36 -0000

--- v3
+++ v4
@@ -25,3 +25,34 @@
 x sam-1.110.jar

 ~~~~
+
+#Usage#
+
+~~~~
+java -jar bamfilter-1.1pre.jar  -q "[query]" -o  -i   --log  [options]
+                        
+Option                                  Description                            
+------                                  -----------   
+-h, --help                              Shows this help message.     
+-v, --version                           Print version info.      
+-i, --input                      A SAM/BAM file with full path 
+-o, --output                    A full path BAM file storing all satisfied SAM records    
+-q, --query                      A string simulated from sql query. All reads satisfied 
+                                        by this query will be report to output file.   
+--log                                   It is compulsory to list you log file with full path here  
+--loglevel                              (Optional)  Logging level required, e.g. INFO, DEBUG. 
+                                        If no parameter is specified, will default to INFO                          
+-f, --filterOut              (Optional) a full path BAM file storing all unsatisfied SAM 
+                                        records. Without this option, all unmatched reads will be discarded.             
+-m, --maxRecordNumber  (Optional) RAM queue size of BAM records during reading and 
+                                        outputting, unit K (eg, 1 equal 1,000 records). default unit will 
+                                        be 100,  that is maximum 100,000 reads.              
+--sort                                  (Optional) specify sort order here [queryname,coordinate,unsorted],     
+                                        here we use unsorted as default.     
+-t, --threadNumber        (Optional) the number of filtering thread is allowed 
+                                        during process. Default number will be 1.            
+--tmpdir                                (Optional) the location of temporary BAMs will created. 
+                                        Default location will depend on picard behaviors      
+--validation                            (Optional)  How strict to read a SAM or BAM. Possible values: 
+                                        {STRICT, LENIENT, SILENT}. Without this option, "LENIENT" will be set.        
+~~~~

qBamfilter modified by q.xu

q.xu — Fri, 23 May 2014 05:00:05 -0000

--- v2
+++ v3
@@ -8,14 +8,14 @@

-* Download the [qsnp tar file](http://sourceforge.net/projects/adamajava/files/qsnp.tar.bz2/download)
+* Download the [qfamfilter tar file](http://sourceforge.net/projects/adamajava/files/qbamfilter.tar/download)
 * Untar the tar file into a directory of your choice
-* current version is 1.0pre.
+* current version is 1.1pre.

 You should see jar files for qsnp and its dependencies:

 ~~~~
-[oholmes@minion0 qsnp]$ tar xjvf qsnp.tar.bz2
+>tar xjvf qfamfilter.tar 
 x antlr-3.2.jar
 x jopt-simple-3.2.jar
 x picard-1.110.jar
@@ -24,6 +24,4 @@
 x qbamfilter-1.1pre.jar
 x sam-1.110.jar

-        
-[oholmes@minion0 qsnp]$
 ~~~~

qBamfilter modified by q.xu

q.xu — Fri, 23 May 2014 04:25:49 -0000

--- v1
+++ v2
@@ -17,17 +17,13 @@
 ~~~~
 [oholmes@minion0 qsnp]$ tar xjvf qsnp.tar.bz2
 x antlr-3.2.jar
-x commons-math3-3.1.1.jar
-x ini4j-0.5.2-SNAPSHOT.jar
 x jopt-simple-3.2.jar
 x picard-1.110.jar
-x qbamfilter-1.0pre.jar
 x qcommon-0.1pre.jar
-x qio-0.1pre.jar
-x qmaths-0.1pre.jar
 x qpicard-0.1pre.jar
-x qsnp-1.0.jar
+x qbamfilter-1.1pre.jar
 x sam-1.110.jar
+
+        
 [oholmes@minion0 qsnp]$
 ~~~~
-

qBamfilter modified by q.xu

q.xu — Fri, 23 May 2014 03:13:36 -0000

Introduction
Installation

Introduction

qbamfilter - reporting all satisfied BAM/SAM record based on a query from input SAM/BAM file to output BAM file. It is optional to report unsatisfied records to specified output BAM

Installation

qbamfilter requires java 7 and (ideally) a multi-core machine (single threads by default). qbamfilter is memory adjustable: You can specify the number of records to store on RAM. It is also designed for fast query execution by specify the number of threads. You can also specify the order method to sort the output BAMs, it creates index file if the output BAM is sorted by coordinate.

Download the qsnp tar file
Untar the tar file into a directory of your choice
current version is 1.0pre.

You should see jar files for qsnp and its dependencies:

[oholmes@minion0 qsnp]$ tar xjvf qsnp.tar.bz2
x antlr-3.2.jar
x commons-math3-3.1.1.jar
x ini4j-0.5.2-SNAPSHOT.jar
x jopt-simple-3.2.jar
x picard-1.110.jar
x qbamfilter-1.0pre.jar
x qcommon-0.1pre.jar
x qio-0.1pre.jar
x qmaths-0.1pre.jar
x qpicard-0.1pre.jar
x qsnp-1.0.jar
x sam-1.110.jar
[oholmes@minion0 qsnp]$