FastqPuri
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Macro definitions. More...
#include <stdint.h>
#include <inttypes.h>
Go to the source code of this file.
Macros | |
#define | B_LEN 131072 |
#define | MAX_FILENAME 300 |
#define | bool int16_t |
#define | true 1 |
#define | false 0 |
#define | max(a, b) (((a) > (b)) ? (a) : (b)) |
#define | min(a, b) (((a) < (b)) ? (a) : (b)) |
#define | mem_usageMB() |
#define | mem_usage() |
#define | DEFAULT_MINQ 27 |
#define | DEFAULT_NTILES 96 |
#define | DEFAULT_NQ 46 |
#define | ZEROQ 33 |
#define | N_ACGT 5 |
#define | MAX_RCOMMAND 4000 |
#define | FA_ENTRY_BUF 20 |
#define | LOG_4 0.60206 |
#define | MIN_NMATCHES 12 |
#define | T_ACGT 4 |
#define | NPOOL_1D 1048576 |
#define | NPOOL_2D 16 |
#define | MAX_FASZ_TREE 1e7 |
#define | BITSPERCHAR 8 |
#define | BASESPERCHAR 4 |
#define | KMER_LEN 25 |
#define | FALSE_POS_RATE 0.05 |
#define | ZERO_POS_RATE 1e-14 |
#define | NO 0 |
#define | ALL 1 |
#define | ENDS 2 |
#define | STRIP 3 |
#define | FRAC 3 |
#define | ENDSFRAC 4 |
#define | GLOBAL 5 |
#define | TREE 1 |
#define | BLOOM 2 |
#define | ERROR 1000 |
#define | DEFAULT_MINL 25 |
#define | ADAP 0 |
#define | CONT 1 |
#define | LOWQ 2 |
#define | NNNN 3 |
#define | GOOD 4 |
#define | NFILTERS 4 |
#define | ADAP2 5 |
#define | CONT2 6 |
#define | LOWQ2 7 |
#define | NNNN2 8 |
#define | GOOD2 9 |
#define | NFILES_DS 10 |
Macro definitions.
#define ADAP 0 |
Adapter filter
#define ADAP2 5 |
Adapter filter read2
#define ALL 1 |
Trims if a lowQ base calling | N is found
#define B_LEN 131072 |
buffer size
#define BASESPERCHAR 4 |
number of nucleotides that can fit in a char
#define BITSPERCHAR 8 |
number of bits in a char
#define BLOOM 2 |
Use a bloom filter to look for contaminations
#define bool int16_t |
define a bool type
#define CONT 1 |
Contamination filter
#define CONT2 6 |
Contamination filter read2
#define DEFAULT_MINL 25 |
Default minimum length under which we discard the reads
#define DEFAULT_MINQ 27 |
Minimum quality threshold
#define DEFAULT_NQ 46 |
Default number of different quality values
#define DEFAULT_NTILES 96 |
Default number of tiles
#define ENDS 2 |
Trims at the ends
#define ENDSFRAC 4 |
trims at the ends and discards a read if the remaining part has more than > percent lowQ bases
#define ERROR 1000 |
Encodes an error when reading in trimN, trimQ, method options in trimFilter
#define FA_ENTRY_BUF 20 |
buffer for fasta entries
#define false 0 |
assign false to 0
#define FALSE_POS_RATE 0.05 |
default false positive rate
#define FRAC 3 |
Discards a read if it contains > percent lowQ bases
#define GLOBAL 5 |
Trims a fixed # bases from e left and right
#define GOOD 4 |
Good reads
#define GOOD2 9 |
Good reads read2
#define KMER_LEN 25 |
default kmer length
#define LOG_4 0.60206 |
log_10(4) for the adapters alignment score
#define LOWQ 2 |
Low quality filter
#define LOWQ2 7 |
Low quality filter read2
#define max | ( | a, | |
b | |||
) | (((a) > (b)) ? (a) : (b)) |
max function
#define MAX_FASZ_TREE 1e7 |
Maximum fasta size for constructing a tree. DECIDE A SENSIBLE SIZE
#define MAX_FILENAME 300 |
Maximum # chars in a filename
#define MAX_RCOMMAND 4000 |
Maximum # chars in R command
#define mem_usage | ( | ) |
#define mem_usageMB | ( | ) |
#define min | ( | a, | |
b | |||
) | (((a) < (b)) ? (a) : (b)) |
min function
#define MIN_NMATCHES 12 |
minimum number of matches demanded
#define N_ACGT 5 |
Number of different nucleotides in the fq file
#define NFILES_DS 10 |
number of outputfiles in double stranded case
#define NFILTERS 4 |
total number of filters
#define NNNN 3 |
N's presence filter
#define NNNN2 8 |
N's presence filter read2
#define NO 0 |
No trimming
#define NPOOL_1D 1048576 |
Number of Node structs allocated in inner dim
#define NPOOL_2D 16 |
Number of *Node allocated in outer dim
#define STRIP 3 |
Looks for the largest N-free sequence
#define T_ACGT 4 |
Number of children per node in tree
#define TREE 1 |
Use a tree to look for contaminations
#define true 1 |
assign true to 1
#define ZERO_POS_RATE 1e-14 |
0 threshold for a double
#define ZEROQ 33 |
ASCII code of lowest quality value (!)