Commit 00ba1cf6 authored by bow's avatar bow
Browse files

Add updates to addres issue #371

parent 37b7f677
......@@ -192,7 +192,7 @@ object ExtractAlignedFastq extends ToolCommand {
opt[String]('r', "interval") required () unbounded () valueName "<interval>" action { (x, c) =>
// yes, we are appending and yes it's O(n) ~ preserving order is more important than speed here
c.copy(intervals = c.intervals :+ x)
} text "Interval strings"
} text "Interval strings (e.g. chr1:1-100)"
opt[File]('i', "in1") required () valueName "<fastq>" action { (x, c) =>
c.copy(inputFastq1 = x)
......@@ -220,7 +220,11 @@ object ExtractAlignedFastq extends ToolCommand {
opt[Int]('s', "read_suffix_length") optional () action { (x, c) =>
c.copy(commonSuffixLength = x)
} text "Length of common suffix from each read pair (default: 0)"
} text
"""Length of suffix mark from each read pair (default: 0). This is used for distinguishing read pairs with
different suffices. For example, if your FASTQ records end with `/1` for the first pair and `/2` for the
second pair, the value of `read_suffix_length` should be 2."
""".stripMargin
note(
"""
......
......@@ -23,7 +23,7 @@ Usage: ExtractAlignedFastq [options]
-I <bam> | --input_file <bam>
Input BAM file
-r <interval> | --interval <interval>
Interval strings
Interval strings (e.g. chr1:1-100)
-i <fastq> | --in1 <fastq>
Input FASTQ file 1
-j <fastq> | --in2 <fastq>
......@@ -35,15 +35,20 @@ Usage: ExtractAlignedFastq [options]
-Q <value> | --min_mapq <value>
Minimum MAPQ of reads in target region to remove (default: 0)
-s <value> | --read_suffix_length <value>
Length of common suffix from each read pair (default: 0)
This tool creates FASTQ file(s) containing reads mapped to the given alignment intervals.
Length of suffix mark from each read pair (default: 0). This is used for distinguishing read pairs with
different suffices. For example, if your FASTQ records end with `/1` for the first pair and `/2` for the
second pair, the value of `read_suffix_length` should be 2.
This tool creates FASTQ file(s) containing reads mapped to the given alignment intervals. A set of FASTQ files that was
used in creating the BAM file is also required since this is used for retrieving full sequences of FASTQ records which
map to the given region. This is useful since some of the records may have undergone modifications such as quality
trimming before alignment. In this case, retrieving the aligned SAM records will only give the modified sequence.
~~~
To run the tool:
~~~
biopet tool ExtractAlignedFastq \
--input_file myBam.bam --in1 myFastq_R1.fastq --out1 myOutFastq_R1.fastq --interval myTarget.bed
--input_file myBam.bam --in1 myFastq_R1.fastq --out1 myOutFastq_R1.fastq --interval chr5:100-200
~~~
* Note that this tool works for single end and paired end data. The above example can be easily extended for paired end data.
The only thing one should add is: `--in2 myFastq_R2.fastq --out2 myOutFastq_R2.fastq`
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment