A command to merge sharded files.
Convert a file with genotypes into corresponding ADAM format and vice versa.
Convert a file with variants into corresponding ADAM format and vice versa.
The adam view
command implements some of the functionality of samtools view
, specifically the -f, -F, -c, and -o
options, in an optionally distributed fashion.
The adam view
command implements some of the functionality of samtools view
, specifically the -f, -F, -c, and -o
options, in an optionally distributed fashion.
It is agnostic to its input and output being SAM, BAM, or ADAM files; when printing to stdout it prints SAM.
Reads2Coverage (accessible as the command 'reads2coverage' through the CLI) takes two arguments, an INPUT and OUTPUT, and calculates the number of reads from INPUT at every location in the file.
Reads2Coverage (accessible as the command 'reads2coverage' through the CLI) takes two arguments, an INPUT and OUTPUT, and calculates the number of reads from INPUT at every location in the file. Optional arguments are only_negative_strands, only_positive_strands and collapse. only_negative_strands and only_positive_strands save coverage computed from only negative and positive strands, respectively. Collapse specifies whether saved coverage should merge neighboring coverage with the same counts to one record.
A command to merge sharded files.
This needs to be a Spark command in order to pull in the Hadoop Config via Spark. Also, this allows us to benefit from Spark's YARN/Mesos submission bits, etc.