FastqPuri
Macros
defines.h File Reference

Macro definitions. More...

#include <stdint.h>
#include <inttypes.h>
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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
 

Detailed Description

Macro definitions.

Author
Paula Perez paula.nosp@m.pere.nosp@m.zrubi.nosp@m.o@gm.nosp@m.ail.c.nosp@m.om
Date
07.08.2017

Macro Definition Documentation

◆ ADAP

#define ADAP   0

Adapter filter

◆ ADAP2

#define ADAP2   5

Adapter filter read2

◆ ALL

#define ALL   1

Trims if a lowQ base calling | N is found

◆ B_LEN

#define B_LEN   131072

buffer size

◆ BASESPERCHAR

#define BASESPERCHAR   4

number of nucleotides that can fit in a char

◆ BITSPERCHAR

#define BITSPERCHAR   8

number of bits in a char

◆ BLOOM

#define BLOOM   2

Use a bloom filter to look for contaminations

◆ bool

#define bool   int16_t

define a bool type

◆ CONT

#define CONT   1

Contamination filter

◆ CONT2

#define CONT2   6

Contamination filter read2

◆ DEFAULT_MINL

#define DEFAULT_MINL   25

Default minimum length under which we discard the reads

◆ DEFAULT_MINQ

#define DEFAULT_MINQ   27

Minimum quality threshold

◆ DEFAULT_NQ

#define DEFAULT_NQ   46

Default number of different quality values

◆ DEFAULT_NTILES

#define DEFAULT_NTILES   96

Default number of tiles

◆ ENDS

#define ENDS   2

Trims at the ends

◆ ENDSFRAC

#define ENDSFRAC   4

trims at the ends and discards a read if the remaining part has more than > percent lowQ bases

◆ ERROR

#define ERROR   1000

Encodes an error when reading in trimN, trimQ, method options in trimFilter

◆ FA_ENTRY_BUF

#define FA_ENTRY_BUF   20

buffer for fasta entries

◆ false

#define false   0

assign false to 0

◆ FALSE_POS_RATE

#define FALSE_POS_RATE   0.05

default false positive rate

◆ FRAC

#define FRAC   3

Discards a read if it contains > percent lowQ bases

◆ GLOBAL

#define GLOBAL   5

Trims a fixed # bases from e left and right

◆ GOOD

#define GOOD   4

Good reads

◆ GOOD2

#define GOOD2   9

Good reads read2

◆ KMER_LEN

#define KMER_LEN   25

default kmer length

◆ LOG_4

#define LOG_4   0.60206

log_10(4) for the adapters alignment score

◆ LOWQ

#define LOWQ   2

Low quality filter

◆ LOWQ2

#define LOWQ2   7

Low quality filter read2

◆ max

#define max (   a,
 
)    (((a) > (b)) ? (a) : (b))

max function

◆ MAX_FASZ_TREE

#define MAX_FASZ_TREE   1e7

Maximum fasta size for constructing a tree. DECIDE A SENSIBLE SIZE

◆ MAX_FILENAME

#define MAX_FILENAME   300

Maximum # chars in a filename

◆ MAX_RCOMMAND

#define MAX_RCOMMAND   4000

Maximum # chars in R command

◆ mem_usage

#define mem_usage ( )
Value:
fprintf(stderr, \
"- Current allocated memory: %" PRIu64 "Bytes.\n", \
uint64_t alloc_mem
Definition: makeBloom.c:42

returns allocated memory in Bytes

◆ mem_usageMB

#define mem_usageMB ( )
Value:
fprintf(stderr, \
"- Current allocated memory: %" PRIu64 "MB.\n", \
alloc_mem >> 20)
uint64_t alloc_mem
Definition: makeBloom.c:42

returns allocated memory in MB

◆ min

#define min (   a,
 
)    (((a) < (b)) ? (a) : (b))

min function

◆ MIN_NMATCHES

#define MIN_NMATCHES   12

minimum number of matches demanded

◆ N_ACGT

#define N_ACGT   5

Number of different nucleotides in the fq file

◆ NFILES_DS

#define NFILES_DS   10

number of outputfiles in double stranded case

◆ NFILTERS

#define NFILTERS   4

total number of filters

◆ NNNN

#define NNNN   3

N's presence filter

◆ NNNN2

#define NNNN2   8

N's presence filter read2

◆ NO

#define NO   0

No trimming

◆ NPOOL_1D

#define NPOOL_1D   1048576

Number of Node structs allocated in inner dim

◆ NPOOL_2D

#define NPOOL_2D   16

Number of *Node allocated in outer dim

◆ STRIP

#define STRIP   3

Looks for the largest N-free sequence

◆ T_ACGT

#define T_ACGT   4

Number of children per node in tree

◆ TREE

#define TREE   1

Use a tree to look for contaminations

◆ true

#define true   1

assign true to 1

◆ ZERO_POS_RATE

#define ZERO_POS_RATE   1e-14

0 threshold for a double

◆ ZEROQ

#define ZEROQ   33

ASCII code of lowest quality value (!)