Below you find a list of the scripts in this package, grouped by rough application situations.

More specific help for each command can be obtained by invoking the respective command with the --help or -h command line argument.

General file and table manipulation

Name	Purpose
add_const_column	Add a column with a column name and fixed value.
cat_tables	Concatenate tables with the same headers.
cross_tab	Print all combinations of input table rows.
fill_template	Output copies of a file, where placeholders are replaced by values read from a table.
index_column	Add a column with a name and a counting number to the table.
merge	Based on values of table 1, look up corresponding rows of table 2 (table join).
pocketR	Change text tables by R commands.
write_later	Cache the input and write it only after input completion, to enable file modification without (explicit) temporary files.

Read sampling and fitering

Name	Purpose
filter_fastq	Apply a program to ID, nucleotide or quality string of each read.
uniform	Sample reads from a reference genome.
synth_fastq	Create a FASTQ file from input IDs, nucleotide strings and quality strings.

Introducing mutations into reads

Name	Purpose
geom_induce	Change bases of input nucleotide strings with a probability dependent of proximity to the string beginning or end.
mapdamage2geomparam	Parse output of mapDamage an output a table of base mutation probabilities.
multiple_mutate	Based on a table of base mutation probabilities, apply multiple mutation rounds to nucleotide strings.
plot_mutation_probabi	lities Plot mutation probability versus base position.

Parallel program calls (e.g. mappers)

Name	Purpose
mcall	Read a list of program calls and invoke several of them in parallel.
table2calls	Based on a table of parameters, generate calls to a script with changing parameters.

SAM parsing and result data handling

Name	Purpose
add_mapped_organisms	Add organisms relating to FASTA record names in the input tables to the output.
plot_read_fate	Plot how many reads from which origin were mapped to which target organism correctly or incorrectly.
plot_parameter_effects	Plot how much mapping parameters influence sensitivity or specificity
sam_extract	Extract information from a SAM file into a text table.
sensspec	Calculate sensitivity and specificity of a mapping run.