A command to merge sharded files.
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.
CalculateDepth (accessible as the command 'depth' through the CLI) takes two arguments, an Read file and a VCF (or equivalent) file, and calculates the number of reads (the 'depth') from the Read file which overlap each of the variants given by the VCF.
CalculateDepth (accessible as the command 'depth' through the CLI) takes two arguments, an Read file and a VCF (or equivalent) file, and calculates the number of reads (the 'depth') from the Read file which overlap each of the variants given by the VCF. It then reports, on standard out, the location and name of each variant along with the calculated depth.
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.
WigFix2Bed (accessible as the command "wigfix2bed" through the CLI) takes fixed wiggle file and converts it to a BED formatted file.
WigFix2Bed (accessible as the command "wigfix2bed" through the CLI) takes fixed wiggle file and converts it to a BED formatted file. The wiggle file is a text based format that implements run-length encoding, without any guarantees where the sync markers are. This makes it difficult to use as a "splittable" format, and necessitates processing the file locally.
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.