int mq_stream_read(mq_stream_t *mqs, void *rdata, int len)
{
int nleft, dpos, nbytes, err;
unsigned char *data = rdata;
if (len == 0) return(0);
nleft = len;
dpos = 0;
err = 0;
do {
nbytes = pack_read(mqs->pack, &(data[dpos]), nleft);
log_printf(2, "msid=%d len=%d nleft=%d dpos=%d nbytes=%d err=%d\n", mqs->msid, len, nleft, dpos, nbytes, err);
if (nbytes >= 0) { //** Read some data
nleft -= nbytes;
dpos += nbytes;
if (nleft > 0) { //** Need to wait for more data
err = mq_stream_read_wait(mqs);
log_printf(2, "msid=%d after read_wait len=%d nleft=%d dpos=%d nbytes=%d err=%d\n", mqs->msid, len, nleft, dpos, nbytes, err);
}
} else {
err = nbytes;
}
} while ((nleft > 0) && (err == 0));
return(err);
}
/******************************************************************************
*
* The main worker node function.
*
* int thread_id: the thread_id
* char *fastq1: FIFO from which bowtie2 can get read1
* char *fastq2: FIFO from which bowtie2 can get read2 (if it exists)
*
*******************************************************************************/
void herd_worker_node(int thread_id, char *fastq1, char *fastq2) {
int cmd_length = 1, max_qname = 0, status, strand;
char *cmd, *last_qname = calloc(1, sizeof(char));
MPI_Header *packed_header;
MPI_read *packed_read = calloc(1, sizeof(MPI_read));
bam_hdr_t *header;
bam1_t *read1 = bam_init1();
bam1_t *read2 = bam_init1();
samFile *fp;
#ifdef DEBUG
MPI_Status stat;
int current_p_size = 100;
htsFile *of;
bam_hdr_t *debug_header = bam_hdr_init();
bam1_t *debug_read = bam_init1();
global_header = bam_hdr_init();
void *p = calloc(100,1);
char *oname = NULL;
#else
int i = 0;
#endif
time_t t0, t1;
int swapped = 0;
assert(last_qname);
assert(packed_read);
//Which strand should we be aligning to?
if(config.directional) {
strand = (thread_id-1) % 2;
} else {
strand = (thread_id-1) % 4;
}
packed_read->size = 0;
packed_read->packed = NULL;
//construct the bowtie2 command
cmd_length += (int) strlen("bowtie2 -q --reorder") + 1;
cmd_length += (int) strlen(config.bowtie2_options) + 1;
cmd_length += (int) strlen("--norc -x") + 1;
cmd_length += (int) strlen(config.genome_dir) + strlen("bisulfite_genome/CT_conversion/BS_CT") + 1;
cmd_length += (int) 2*(strlen("-1 ") + strlen(fastq1)) + 3;
if(config.paired) cmd_length += (int) strlen(fastq2); //This is likely unneeded.
#ifdef DEBUG
oname = malloc(sizeof(char) *(1+strlen(config.odir)+strlen(config.basename)+strlen("_X.bam")));
assert(oname);
sprintf(oname, "%s%s_%i.bam", config.odir, config.basename, thread_id);
if(!config.quiet) fprintf(stderr, "Writing output to %s\n", oname);
of = sam_open(oname, "wb");
free(oname);
#endif
cmd = (char *) malloc(sizeof(char) * cmd_length);
assert(cmd);
if(strand == 0) { //OT Read#1 C->T, Read#2 G->A, Genome C->T only the + strand
if(config.paired) {
sprintf(cmd, "bowtie2 -q --reorder %s --norc -x %sbisulfite_genome/CT_conversion/BS_CT -1 %s -2 %s", config.bowtie2_options, config.genome_dir, fastq1, fastq2);
} else {
sprintf(cmd, "bowtie2 -q --reorder %s --norc -x %sbisulfite_genome/CT_conversion/BS_CT -U %s", config.bowtie2_options, config.genome_dir, fastq1);
}
} else if(strand == 1) { //OB Read#1 C->T, Read#2 G->A, Genome G->A only the - strand
if(config.paired) {
sprintf(cmd, "bowtie2 -q --reorder %s --nofw -x %sbisulfite_genome/GA_conversion/BS_GA -1 %s -2 %s", config.bowtie2_options, config.genome_dir, fastq1, fastq2);
} else {
sprintf(cmd, "bowtie2 -q --reorder %s --nofw -x %sbisulfite_genome/GA_conversion/BS_GA -U %s", config.bowtie2_options, config.genome_dir, fastq1);
}
} else if(strand == 2) { //CTOT Read#1 G->A, Read#2 C->T, Genome C->T, only the - strand
if(config.paired) {
sprintf(cmd, "bowtie2 -q --reorder %s --nofw -x %sbisulfite_genome/CT_conversion/BS_CT -1 %s -2 %s", config.bowtie2_options, config.genome_dir, fastq1, fastq2);
} else {
sprintf(cmd, "bowtie2 -q --reorder %s --nofw -x %sbisulfite_genome/CT_conversion/BS_CT -U %s", config.bowtie2_options, config.genome_dir, fastq1);
}
} else if(strand == 3) { //CTOB Read#1 G->A, Read#2 C->T, Genome G->A, only the + strand
if(config.paired) {
sprintf(cmd, "bowtie2 -q --reorder %s --norc -x %sbisulfite_genome/GA_conversion/BS_GA -1 %s -2 %s", config.bowtie2_options, config.genome_dir, fastq1, fastq2);
} else {
sprintf(cmd, "bowtie2 -q --reorder %s --norc -x %sbisulfite_genome/GA_conversion/BS_GA -U %s", config.bowtie2_options, config.genome_dir, fastq1);
}
} else {
fprintf(stderr, "Oh shit, got strand %i!\n", strand);
return;
}
//Start the process
if(!config.quiet) fprintf(stderr, "Node %i executing: %s\n", thread_id, cmd); fflush(stderr);
fp = sam_popen(cmd);
header = sam_hdr_read(fp);
#ifdef DEBUG
sam_hdr_write(of, header);
#endif
#ifndef DEBUG
packed_header = pack_header(header);
if(thread_id == 1) {
//Send the header
MPI_Send((void *) &(packed_header->size), 1, MPI_INT, 0, 1, MPI_COMM_WORLD);
status = MPI_Send((void *) packed_header->packed, packed_header->size, MPI_BYTE, 0, 2, MPI_COMM_WORLD);
if(status != MPI_SUCCESS) {
fprintf(stderr, "MPI_Send returned %i\n", status);
fflush(stderr);
}
}
#else
packed_header = pack_header(header);
void *tmp_pointer = malloc(packed_header->size);
assert(tmp_pointer);
MPI_Request request;
MPI_Isend((void *) packed_header->packed, packed_header->size, MPI_BYTE, 0, 2, MPI_COMM_WORLD, &request);
status = MPI_Recv(tmp_pointer, packed_header->size, MPI_BYTE, 0, 2, MPI_COMM_WORLD, &stat);
if(status != MPI_SUCCESS) fprintf(stderr, "We seem to have not been able to send the message to ourselves!\n");
MPI_Wait(&request, &stat);
unpack_header(debug_header, tmp_pointer);
global_header = debug_header;
free(tmp_pointer);
#endif
t0 = time(NULL);
if(!config.quiet) fprintf(stderr, "Node %i began sending reads @%s", thread_id, ctime(&t0)); fflush(stderr);
while(sam_read1(fp, header, read1) >= 0) {
#ifdef DEBUG
sam_write1(of, global_header, read1);
#endif
if(strcmp(bam_get_qname(read1), last_qname) == 0) { //Multimapper
if(config.paired) {
sam_read1(fp, header, read2);
#ifdef DEBUG
sam_write1(of, global_header, read2);
#endif
}
continue;
} else {
if(read1->core.l_qname > max_qname) {
max_qname = read1->core.l_qname + 10;
last_qname = realloc(last_qname, sizeof(char) * max_qname);
assert(last_qname);
}
strcpy(last_qname, bam_get_qname(read1));
}
//Are paired-end reads in the wrong order?
swapped = 0;
if(config.paired) {
if(read1->core.flag & BAM_FREAD2) {
swapped = 1;
sam_read1(fp, header, read2);
packed_read = pack_read(read2, packed_read);
#ifndef DEBUG
MPI_Send((void *) packed_read->packed, packed_read->size, MPI_BYTE, 0, 5, MPI_COMM_WORLD);
#else
sam_write1(of, global_header, read2);
if(packed_read->size > current_p_size) {
p = realloc(p, packed_read->size);
assert(p);
}
MPI_Isend((void *) packed_read->packed, packed_read->size, MPI_BYTE, 0, 5, MPI_COMM_WORLD, &request);
status = MPI_Recv(p, packed_read->size, MPI_BYTE, 0, 5, MPI_COMM_WORLD, &stat);
MPI_Wait(&request, &stat);
debug_read = unpack_read(debug_read, p);
#endif
}
}
//Send the read
packed_read = pack_read(read1, packed_read);
#ifndef DEBUG
MPI_Send((void *) packed_read->packed, packed_read->size, MPI_BYTE, 0, 5, MPI_COMM_WORLD);
#else
if(packed_read->size > current_p_size) {
p = realloc(p, packed_read->size);
assert(p);
}
MPI_Isend(packed_read->packed, packed_read->size, MPI_BYTE, 0, 5, MPI_COMM_WORLD, &request);
status = MPI_Recv(p, packed_header->size, MPI_BYTE, 0, 5, MPI_COMM_WORLD, &stat);
MPI_Wait(&request, &stat);
#endif
//Deal with paired-end reads
if(config.paired && !swapped) {
sam_read1(fp, header, read2);
packed_read = pack_read(read2, packed_read);
#ifndef DEBUG
MPI_Send((void *) packed_read->packed, packed_read->size, MPI_BYTE, 0, 5, MPI_COMM_WORLD);
#else
sam_write1(of, global_header, read2);
if(packed_read->size > current_p_size) {
p = realloc(p, packed_read->size);
assert(p);
}
MPI_Isend((void *) packed_read->packed, packed_read->size, MPI_BYTE, 0, 5, MPI_COMM_WORLD, &request);
status = MPI_Recv(p, packed_header->size, MPI_BYTE, 0, 5, MPI_COMM_WORLD, &stat);
MPI_Wait(&request, &stat);
debug_read = unpack_read(debug_read, p);
#endif
}
#ifndef DEBUG
i++;
#endif
}
t1 = time(NULL);
if(!config.quiet) fprintf(stderr, "Node %i finished sending reads @%s\t(%f sec elapsed)\n", thread_id, ctime(&t1), difftime(t1, t0)); fflush(stderr);
//Notify the master node
packed_read->size = 0;
#ifndef DEBUG
void *A = malloc(1);
assert(A);
MPI_Send(A, 1, MPI_BYTE, 0, 5, MPI_COMM_WORLD);
free(A);
#endif
//Close things up
bam_hdr_destroy(header);
bam_destroy1(read1);
bam_destroy1(read2);
free(cmd);
if(packed_read->packed != NULL) free(packed_read->packed);
free(packed_read);
if(packed_header->packed != NULL) free(packed_header->packed);
free(packed_header);
free(last_qname);
sam_pclose(fp);
//Remove the FIFO(s)
unlink(fastq1);
if(config.paired) unlink(fastq2);
#ifdef DEBUG
sam_close(of);
bam_hdr_destroy(debug_header);
bam_destroy1(debug_read);
free(p);
#endif
if(!config.quiet) fprintf(stderr, "Exiting worker node %i\n", thread_id); fflush(stderr);
};
