cljam.tools.cli — cljam 0.8.5

Implementations of the command-line tool.

convert clj

(convert args)

Parses command line args and converts file format based on the file extension.

dict clj

(dict args)

Parses command line args and make fasta dictionary file.

faidx clj

(faidx args)

Parses command line args and make fasta index.

index clj

(index args)

Parses command line args and creates index file.

level clj

(level args)

Parses command line args and adds level of alignments.

normalize clj

(normalize args)

Parses command line args and normalizes references of the SAM/BAM format.

pileup clj

(pileup args)

Parses command line args and pileups BAM file.

run clj

(run args)

Executes the specified subcommand.

sort clj

(sort args)

Parses command line args and sorts alignments by the specified method.

version clj

(version _)

Prints this software version.

view clj

(view args)

Parses command line args and prints all or sub alignments of input sam/bam.