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fastq_count_kthread.c
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fastq_count_kthread.c
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//gcc -g -O3 -Wall klib/kthread.c fastq_count_kthread.c -o fastq_count_kthread -lz -lpthread
//gcc -g -O3 -Wall klib-master/kthread.c fastq_count_kthread.c -o fastq_count_kthread -I/share/software/software/zlib_1.2.8_install/include -L/share/software/software/zlib_1.2.8_install/lib -lz -lpthread
#include "IO_stream.h"
#include <stdlib.h>
#include <stdint.h>
#include <time.h>
#include <pthread.h>
#include <sys/time.h>
#include <unistd.h>
#include <libgen.h>
#define CPU_NUM sysconf(_SC_NPROCESSORS_ONLN)
#define Alloc2DArray(Array,nrow,ncol) \
do{ \
Array=(uint64_t **)calloc(nrow,sizeof(uint64_t *)); \
uint32_t index=0; \
for (;index < nrow;index++ ){ \
*(Array+index)=(uint64_t *)calloc(ncol,sizeof(uint64_t)); \
} \
}while (0)
#define Free2DArray(Array,nrow) \
do{ \
uint32_t index; \
for (index=0;index < nrow;index++ ){ \
free(*(Array+index)); \
} \
free(Array); \
}while (0)
#define AssignQuality(Array,Q,Len) \
do{ \
uint32_t index; \
for(index=0;index<Len;index++){ \
(*(*(Array+(uint8_t)*(Q+index))+index))++; \
} \
}while (0)
#define statQ(Array,nrow,ncol,sum,Q1,sumQ1,Q2,sumQ2) \
do{ \
uint32_t ii=0,jj=0; \
for(ii=0;ii<nrow;ii++){ \
for (jj=0;jj<ncol ;jj++ ){ \
sum += *(*(Array+ii)+jj); \
if (ii >=Q1) sumQ1 += Array[ii][jj]; \
if (ii >=Q2) sumQ2 += Array[ii][jj]; \
} \
} \
}while (0)
#define printQ(Array,nrow,ncol,stream) \
do{ \
uint32_t ii=0,jj=0; \
for(ii=0;ii<nrow;ii++){ \
for (jj=0;jj<ncol ;jj++ ){ \
if(jj==ncol-1){ \
fprintf(stream,"%lu\n",Array[ii][jj]); \
}else{ \
fprintf(stream,"%lu\t",Array[ii][jj]); \
} \
} \
} \
}while (0)
#define printSeqLen(Array,n,stream,minLen,maxLen) \
do{ \
uint32_t index; \
fprintf(stream,"#Len:"); \
for (index=minLen;index <= maxLen;index++ ){ \
fprintf(stream,"\t%u",index); \
} \
fprintf(stream,"\n#Freq:"); \
for (index=minLen;index <= maxLen;index++ ){ \
fprintf(stream,"\t%lu",*(Array+index)); \
} \
fprintf(stream,"\n"); \
}while (0)
#define statSeqLen(Array,n,minLen,maxLen,meanLen,sumFreq) \
do{ \
uint32_t index; \
for (index=0;index < n;index++ ){ \
if (*(Array+index)){ \
(sumFreq)+=*(Array+index); \
(meanLen)+=1.0*(*(Array+index))*index; \
if (!(minLen)) (minLen)=index; \
if ((maxLen)<index) (maxLen)=index; \
} \
} \
}while (0)
struct globalArgs_t {
char **infiles;
const char *outfile;
int numInfiles;
int thread;
int header;
int LengthDetail;
} globalArgs;
typedef struct _thread_arg_
{
char **infiles;
FILE **out;
uint32_t *read_count;
uint32_t *minLen;
uint32_t *maxLen;
uint64_t **SeqLen;
uint64_t ***Quality;
double *mean_len;
}thread_arg_t;
void load_fq(void *data,long i,int tid);
static inline void display_usage(char * argv[]);
void count_read(gzFile fq,uint32_t *sumFreq,uint32_t *minLen,uint32_t *maxLen,uint64_t *SeqLen,uint64_t **Quality,const char *infile,FILE *out,double *mean_length);
static inline long long usec(void);
void kt_for(int n_threads, void (*func)(void*,long,int), void *data, long n);
long long usec(void){
struct timeval tv;
gettimeofday(&tv,NULL);
return (((long long)tv.tv_sec)*1000000)+tv.tv_usec;
}
void count_read(gzFile fq,uint32_t *sumFreq,uint32_t *minLen,uint32_t *maxLen,uint64_t *SeqLen,uint64_t **Quality,const char *infile,FILE *out,double *mean_length){
char *buf=(char *)calloc(1024,sizeof(char));
uint64_t sum=0,sumQ1=0,sumQ2=0;
while (gzgets(fq,buf,1024*sizeof(char))!=NULL){
gzgets(fq,buf,1024*sizeof(char));
uint16_t seqLen=strlen(buf)-1;
(*(SeqLen+seqLen))++;
gzgets(fq,buf,1024*sizeof(char));
gzgets(fq,buf,1024*sizeof(char));
AssignQuality(Quality,buf,seqLen);
}
free(buf);
statSeqLen(SeqLen,512,*minLen,*maxLen,*mean_length,*sumFreq);
double Mean_Len=*mean_length/(*sumFreq);
statQ(Quality,128,512,sum,53,sumQ1,63,sumQ2);
if (globalArgs.header) fprintf(out,"#Filename\tReadCount\tBaseCount\tMeanLen\tMinLen\tMaxLen\tQ20(%%)\tQ30(%%)\n");
fprintf(out,"%s\t%u\t%.0f\t%.0f\t%u\t%u\t%.3f\t%.3f\n",infile,*sumFreq,*mean_length,Mean_Len,*minLen,*maxLen,1.0*sumQ1/sum*100,1.0*sumQ2/sum*100);
if (globalArgs.LengthDetail){
printSeqLen(SeqLen,512,out,*minLen,*maxLen);
printQ(Quality,128,*maxLen,out);
}
}
void display_usage(char * argv[]){
char *buffer=(char* )malloc(10240*sizeof(char));
const char* usage=
"\nCopyright (c) InfiniGenomics 2016\n" \
"Contact: XiongXu <[email protected]> <[email protected]> \n" \
"Discription:\n This program is used for counting the read count with or without gzip compressed fastq files .\n" \
"Usage: %s file1.fq file2.fq ... [-o outfile] [-t thread] [-H] [-L] [-h] \n" \
"Example1:\n %s /share/seq_dir1/Item/prenatal/140129_SN1116_0776_AC2WTGACXX/13C37198_L7_I012.R1.clean.fastq.gz \n" \
"\n" \
" [-o OUTPUT] = OUTPUT file.default is stdout. [option]\n" \
" [-H ] = ouput the Header information. [option]\n" \
" [-L ] = ouput the read length in detail to the OUTPUT [option]\n" \
" [-t ] = thread .default is the Infiles' number,if Infiles' number \n" \
" > cpu cores,then the default is the cpu core number [option]\n" \
" [-h ] This helpful help screen. [option]\n" \
" Infiles = Infile1,Infile2... [required]\n" \
"\n";
sprintf(buffer,usage,argv[0],argv[0]);
fprintf(stderr,"%s",buffer);
free(buffer);
exit(1);
}
void load_fq(void *data,long i,int tid){
//fprintf(stderr,"tid: %d\n",tid);
thread_arg_t *thread_arg=(thread_arg_t *)data;
gzFile fq=open_input_stream(thread_arg->infiles[i]);
count_read(fq,&thread_arg->read_count[i],&thread_arg->minLen[i],&thread_arg->maxLen[i],thread_arg->SeqLen[i],thread_arg->Quality[i],thread_arg->infiles[i],thread_arg->out[i],&thread_arg->mean_len[i]);
gzclose(fq);
}
void reduceStats(void *data,int n,FILE *out){
thread_arg_t *thread_arg=(thread_arg_t *)data;
uint32_t i,j,k,sumRC=0,TotalMinLen=10000,TotalMaxLen=0;
uint64_t *sumSeqLen=(uint64_t *)calloc(512,sizeof(uint64_t)),**sumQuality=NULL,sum=0,sumQ1=0,sumQ2=0;
Alloc2DArray(sumQuality,128,512);
double sumBC=0,TotalMeanLen;
for (i=0;i<(uint32_t)n;i++){
sumRC+=thread_arg->read_count[i];
sumBC+=thread_arg->mean_len[i];
if (thread_arg->minLen[i]<TotalMinLen) TotalMinLen=thread_arg->minLen[i];
if (thread_arg->maxLen[i]>TotalMaxLen) TotalMaxLen=thread_arg->maxLen[i];
for(j=0;j<128;j++){
for(k=0;k<512;k++){
sumQuality[j][k]+=thread_arg->Quality[i][j][k];
}
}
for(j=0;j<512;j++){
sumSeqLen[j]+=thread_arg->SeqLen[i][j];
}
}
statQ(sumQuality,128,512,sum,53,sumQ1,63,sumQ2);
TotalMeanLen=sumBC/sumRC;
if (globalArgs.header) fprintf(out,"#ReadCount\tBaseCount\tMeanLen\tMinLen\tMaxLen\tQ20(%%)\tQ30(%%)\n");
fprintf(out,"%u\t%.0f\t%.0f\t%u\t%u\t%.3f\t%.3f\n",sumRC,sumBC,TotalMeanLen,TotalMinLen,TotalMaxLen,1.0*sumQ1/sum*100,1.0*sumQ2/sum*100);
if (globalArgs.LengthDetail){
printSeqLen(sumSeqLen,512,out,TotalMinLen,TotalMaxLen);
printQ(sumQuality,128,TotalMaxLen,out);
}
Free2DArray(sumQuality,128);
free(sumSeqLen);
}
int main(int argc, char *argv[]) {
int opt = 0;
globalArgs.infiles=NULL;
globalArgs.numInfiles=0;
globalArgs.header=0;
globalArgs.LengthDetail=0;
globalArgs.outfile="-";
globalArgs.thread=CPU_NUM;
const char *optString = "o:t:HLh?";
opt = getopt( argc, argv, optString );
while( opt != -1 ) {
switch( opt ) {
case 'o':
globalArgs.outfile = optarg;
break;
case 't':
globalArgs.thread = atoi(optarg);
break;
case 'H':
globalArgs.header++;
break;
case 'L':
globalArgs.LengthDetail++;
break;
case '?': /* fall-through is intentional */
case 'h':
display_usage(argv);
break;
default:
fprintf(stderr,"error parameter!\n");
break;
}
opt = getopt( argc, argv, optString );
}
globalArgs.infiles = argv + optind;
globalArgs.numInfiles = argc - optind;
if (globalArgs.numInfiles<globalArgs.thread ) globalArgs.thread=globalArgs.numInfiles;
long long begin=usec();
char suffix_buf[32]={0};
int i;
if (globalArgs.numInfiles){
thread_arg_t *args=(thread_arg_t *)calloc(globalArgs.numInfiles,sizeof(thread_arg_t));
args->infiles=globalArgs.infiles;
args->mean_len=(double *)calloc(globalArgs.numInfiles,sizeof(double *));
args->read_count=(uint32_t *)calloc(globalArgs.numInfiles,sizeof(uint32_t));
args->minLen=(uint32_t *)calloc(globalArgs.numInfiles,sizeof(uint32_t));
args->maxLen=(uint32_t *)calloc(globalArgs.numInfiles,sizeof(uint32_t));
args->SeqLen=(uint64_t **)calloc(globalArgs.numInfiles,sizeof(uint64_t *));
args->Quality=(uint64_t ***)calloc(globalArgs.numInfiles,sizeof(uint64_t **));
args->out=(FILE **)calloc(globalArgs.numInfiles,sizeof(FILE *));
for(i=0;i<globalArgs.numInfiles;i++){
sprintf(suffix_buf,".%d.tsv",i);
args->out[i]=fcreat_outfile(basename(globalArgs.infiles[i]),suffix_buf);
args->SeqLen[i]=(uint64_t *)calloc(512,sizeof(uint64_t));
Alloc2DArray(args->Quality[i],128,512);
}
kt_for(globalArgs.thread, load_fq, args, globalArgs.numInfiles);
if(globalArgs.numInfiles >=1) {
FILE *Out=fopen_output_stream(globalArgs.outfile);
reduceStats(args,globalArgs.numInfiles,Out);
fclose(Out);
}
free(args->mean_len);
free(args->read_count);
free(args->minLen);
free(args->maxLen);
for(i=0;i<globalArgs.numInfiles;i++){
free(args->SeqLen[i]);
fclose(args->out[i]);
Free2DArray(args->Quality[i],128);
}
free(args->SeqLen);
free(args->Quality);
free(args->out);
free(args);
}
fprintf(stderr,"Finished at %.3f s\n",(double)(usec()-begin)/CLOCKS_PER_SEC);
return 0;
}