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Public Attributes

mer_counter_args Struct Reference

Where the command line options are stored. More...

#include <mer_counter_cmdline.hpp>

List of all members.

Public Attributes

int both_flag
 Write list and raw database (default=off).
unsigned int both_given
 Whether both was given.
const char * both_help
 Write list and raw database help description.
int both_strands_flag
 Count both strand, canonical representation (default=off).
unsigned int both_strands_given
 Whether both-strands was given.
const char * both_strands_help
 Count both strand, canonical representation help description.
long buffer_size_arg
 Size of buffers (default='8192').
unsigned int buffer_size_given
 Whether buffer-size was given.
const char * buffer_size_help
 Size of buffers help description.
char * buffer_size_orig
 Size of buffers original value given at command line.
long buffers_arg
 Number of buffers per thread.
unsigned int buffers_given
 Whether buffers was given.
const char * buffers_help
 Number of buffers per thread help description.
char * buffers_orig
 Number of buffers per thread original value given at command line.
int counter_len_arg
 Length of counting field (default='7').
unsigned int counter_len_given
 Whether counter-len was given.
const char * counter_len_help
 Length of counting field help description.
char * counter_len_orig
 Length of counting field original value given at command line.
unsigned int full_help_given
 Whether full-help was given.
const char * full_help_help
 Print help, including hidden options, and exit help description.
unsigned int help_given
 Whether help was given.
const char * help_help
 Print help and exit help description.
char ** inputs
 unamed options (options without names)
unsigned inputs_num
 unamed options number
int lock_flag
 Lock hash in memory (no swapping) (default=off).
unsigned int lock_given
 Whether lock was given.
const char * lock_help
 Lock hash in memory (no swapping) help description.
long lower_count_arg
 Don't output k-mer with count < lower-count.
unsigned int lower_count_given
 Whether lower-count was given.
const char * lower_count_help
 Don't output k-mer with count < lower-count help description.
char * lower_count_orig
 Don't output k-mer with count < lower-count original value given at command line.
char * matrix_arg
 Hash function binary matrix.
unsigned int matrix_given
 Whether matrix was given.
const char * matrix_help
 Hash function binary matrix help description.
char * matrix_orig
 Hash function binary matrix original value given at command line.
int measure_flag
 Write usage statistics (default=off).
unsigned int measure_given
 Whether measure was given.
const char * measure_help
 Write usage statistics help description.
int mer_len_arg
 Length of mer.
unsigned int mer_len_given
 Whether mer-len was given.
const char * mer_len_help
 Length of mer help description.
char * mer_len_orig
 Length of mer original value given at command line.
int min_quality_arg
 Minimum quality. A base with lesser quality becomes an N (default='0').
unsigned int min_quality_given
 Whether min-quality was given.
const char * min_quality_help
 Minimum quality. A base with lesser quality becomes an N help description.
char * min_quality_orig
 Minimum quality. A base with lesser quality becomes an N original value given at command line.
int no_write_flag
 Don't write database (default=off).
unsigned int no_write_given
 Whether no-write was given.
const char * no_write_help
 Don't write database help description.
long out_buffer_size_arg
 Size of output buffer per thread (default='20000000').
unsigned int out_buffer_size_given
 Whether out-buffer-size was given.
const char * out_buffer_size_help
 Size of output buffer per thread help description.
char * out_buffer_size_orig
 Size of output buffer per thread original value given at command line.
int out_counter_len_arg
 Length of counter field in output (default='4').
unsigned int out_counter_len_given
 Whether out-counter-len was given.
const char * out_counter_len_help
 Length of counter field in output help description.
char * out_counter_len_orig
 Length of counter field in output original value given at command line.
char * output_arg
 Output prefix (default='mer_counts').
unsigned int output_given
 Whether output was given.
const char * output_help
 Output prefix help description.
char * output_orig
 Output prefix original value given at command line.
int quake_flag
 Quake compatibility mode (default=off).
unsigned int quake_given
 Whether quake was given.
const char * quake_help
 Quake compatibility mode help description.
int quality_start_arg
 Starting ASCII for quality values (default='64').
unsigned int quality_start_given
 Whether quality-start was given.
const char * quality_start_help
 Starting ASCII for quality values help description.
char * quality_start_orig
 Starting ASCII for quality values original value given at command line.
int raw_flag
 Write raw database (default=off).
unsigned int raw_given
 Whether raw was given.
const char * raw_help
 Write raw database help description.
int reprobes_arg
 Maximum number of reprobes (default='62').
unsigned int reprobes_given
 Whether reprobes was given.
const char * reprobes_help
 Maximum number of reprobes help description.
char * reprobes_orig
 Maximum number of reprobes original value given at command line.
long size_arg
 Hash size.
unsigned int size_given
 Whether size was given.
const char * size_help
 Hash size help description.
char * size_orig
 Hash size original value given at command line.
char * stats_arg
 Print stats.
unsigned int stats_given
 Whether stats was given.
const char * stats_help
 Print stats help description.
char * stats_orig
 Print stats original value given at command line.
int stream_flag
 Read from stream, not memory map (default=off).
unsigned int stream_given
 Whether stream was given.
const char * stream_help
 Read from stream, not memory map help description.
int threads_arg
 Number of threads (default='1').
unsigned int threads_given
 Whether threads was given.
const char * threads_help
 Number of threads help description.
char * threads_orig
 Number of threads original value given at command line.
char * timing_arg
 Print timing information.
unsigned int timing_given
 Whether timing was given.
const char * timing_help
 Print timing information help description.
char * timing_orig
 Print timing information original value given at command line.
long upper_count_arg
 Don't output k-mer with count > upper-count.
unsigned int upper_count_given
 Whether upper-count was given.
const char * upper_count_help
 Don't output k-mer with count > upper-count help description.
char * upper_count_orig
 Don't output k-mer with count > upper-count original value given at command line.
unsigned int version_given
 Whether version was given.
const char * version_help
 Print version and exit help description.

Detailed Description

Where the command line options are stored.

Definition at line 38 of file mer_counter_cmdline.hpp.


The documentation for this struct was generated from the following file:

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