@groovy.util.logging.Log class ExtractFASTQ extends java.lang.Object
Extract reads as pairs from a sorted BAM and writes them out to standard output in interleaved format.
Example:
gngstool ExtractFASTQ -bam my.bam -L chr1:5000000-6000000 > interleaved.fastq
An example of realigning a portion of a BAM file:
gngstool ExtractFASTQ -bam my.bam -L chr1:5000000-6000000 | \
bwa mem -p ref.fa - | \
samtools view -bSu - | \
samtools sort -o out.bam
| Type | Name and description |
|---|---|
boolean |
addPositionToNames |
SAM |
bam |
int |
concurrency |
java.io.Writer |
out |
Regions |
regions |
int |
spoolSize |
| Constructor and description |
|---|
ExtractFASTQ
(SAM bam, Regions regions) |
| Type Params | Return Type | Name and description |
|---|---|---|
|
static Regions |
getGeneRegions(java.lang.String genomeVersion, java.util.List<java.lang.String> genes)Attempt to interpret the given list of genes as either a list of gene symbols or a text file specifying the genes to read. |
|
static void |
main(java.lang.String[] args) |
|
void |
run(java.io.Writer out) |
| Methods inherited from class | Name |
|---|---|
class java.lang.Object |
java.lang.Object#wait(long), java.lang.Object#wait(long, int), java.lang.Object#wait(), java.lang.Object#equals(java.lang.Object), java.lang.Object#toString(), java.lang.Object#hashCode(), java.lang.Object#getClass(), java.lang.Object#notify(), java.lang.Object#notifyAll() |
Attempt to interpret the given list of genes as either a list of gene symbols or a text file specifying the genes to read. @return
Groovy Documentation