| setUseReducer(boolean) |
False |
-r |
Use a reducer to generate one output SAM file. |
| setPartitionNumber(int) |
Auto |
none |-partitions <num>
|
By default, data is split into pieces of HDFS block size. Otherwise, input data is split into num partitions. |
| setSortFastqReads(int) |
Join |
none |-sort |-sorthdfs
|
Set the RDDs creation approach for paired-end reads: Join (0), Join & sortByKey (1) or SortHDFS (2). |
| setNumThreads(int) |
1 |
-threads <num> |
If num > 1, hybrid parallelism mode is enabled in such a way that each map process is executed using num threads. |
| setAlgorithm(int) |
BWA-MEM |
-mem |-aln |-bwasw
|
Set the alignment algorithm: BWA-MEM (0), BWA-backtrack (1), BWA-SW (2) |
| setPairedReads(boolean) |
Paired |
-paired |-single
|
Use single-end (one FASTQ input file) or paired-end reads (two FASTQ input files). |
| setIndexPath(string) |
– |
-index <prefix> |
Set the path to the reference genome (mandatory option). |
| setInputPath(string) |
– |
Positional |
Set the path (in HDFS) to the FASTQ input file (mandatory option for single-end and paired-end reads). |
| setInputPath2(string) |
– |
Positional |
Set the path (in HDFS) to the second FASTQ input file (mandatory option for paired-end reads). |
| setOutputPath(string) |
– |
Positional |
Set the location (in HDFS) where the output SAM file/s will be stored. |
