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The genome directory should always end in /, but that was not made cl…
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…ear previously. That has been fixed and now one should not actually have to end the directory name with a /
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@dpryan79
dpryan79 committed Feb 27, 2014
1 parent 706ecee commit 0c79e51
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Showing 6 changed files with 42 additions and 11 deletions.
9 changes: 7 additions & 2 deletions auxiliary/CpG_coverage.c
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ void next_line(FILE *fp, char *buffer) {
}

void usage(char *prog) {
printf("Usage: %s [OPTIONS] genome_directory input.bedGraph output.txt\n", prog);
printf("Usage: %s [OPTIONS] genome_directory/ input.bedGraph output.txt\n", prog);
printf("\n\
Calculate a histogram of per-CpG coverage. N.B., the genome and bedGraph\n\
file need to be in the same order (they will be if the bedGraph file was\n\
Expand Down Expand Up @@ -69,7 +69,11 @@ int main(int argc, char *argv[]) {
i++;
chromosomes.max_genome = strtoull(argv[i], NULL, 10);
} else if(config.genome_dir == NULL) {
config.genome_dir = argv[i];
config.genome_dir = strdup(argv[i]);
if(*(config.genome_dir+strlen(config.genome_dir)-1) != '/') {
config.genome_dir = realloc(config.genome_dir, sizeof(char) * (strlen(config.genome_dir)+2));
sprintf(config.genome_dir, "%s/", config.genome_dir);
}
} else if(iname == NULL) {
iname = argv[i];
} else if(oname == NULL) {
Expand Down Expand Up @@ -139,6 +143,7 @@ int main(int argc, char *argv[]) {
printf("There were %llu CpGs\n", nCpGs);

//Close things up
if(config.genome_dir != NULL) free(config.genome_dir);
free(line);
free(chromosomes.genome);
for(i=0; i<chromosomes.nchromosomes; i++) {
Expand Down
9 changes: 7 additions & 2 deletions auxiliary/bedGraph2methylKit.c
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ struct CpG {
};

void usage(char *prog) {
printf("Usage: %s [OPTIONS] genome_directory file.bedGraph\n", prog);
printf("Usage: %s [OPTIONS] genome_directory/ file.bedGraph\n", prog);
printf("\n\
Convert a CpG bedGraph file to the format required for methylKit.\n\
The CpGs in the file should not be merged (i.e., they should represent\n\
Expand Down Expand Up @@ -104,7 +104,11 @@ int main(int argc, char *argv[]) {
usage(argv[0]);
return 0;
} else if(config.genome_dir == NULL) {
config.genome_dir = argv[i];
config.genome_dir = strdup(argv[i]);
if(*(config.genome_dir+strlen(config.genome_dir)-1) != '/') {
config.genome_dir = realloc(config.genome_dir, sizeof(char) * (strlen(config.genome_dir)+2));
sprintf(config.genome_dir, "%s/", config.genome_dir);
}
} else if(fname == NULL) {
fname = argv[i];
} else if(strcmp(argv[i], "--genome-size") == 0) {
Expand Down Expand Up @@ -159,6 +163,7 @@ int main(int argc, char *argv[]) {
}

//Close things up
if(config.genome_dir != NULL) free(config.genome_dir);
free(line);
fclose(of);
fclose(ifile);
Expand Down
9 changes: 7 additions & 2 deletions auxiliary/merge_CpGs.c
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ struct CpG {
};

void usage(char *prog) {
printf("Usage: %s [OPTIONS] genome_directory file.bedGraph [file2.bedGraph file3.bedGraph]\n", prog);
printf("Usage: %s [OPTIONS] genome_directory/ file.bedGraph [file2.bedGraph file3.bedGraph]\n", prog);
printf("\n\
Merge strand metrics for individual CpG calls (i.e. if there are separate\n\
methylation metrics for the C's on the + and - strand of a CpG site, combine\n\
Expand Down Expand Up @@ -112,7 +112,11 @@ int main(int argc, char *argv[]) {
} else if(strcmp(argv[i], "--genome-size") == 0) {
chromosomes.max_genome = strtoull(argv[++i], NULL, 10);
} else if(config.genome_dir == NULL) {
config.genome_dir = argv[i];
config.genome_dir = strdup(argv[i]);
if(*(config.genome_dir+strlen(config.genome_dir)-1) != '/') {
config.genome_dir = realloc(config.genome_dir, sizeof(char) * (strlen(config.genome_dir)+2));
sprintf(config.genome_dir, "%s/", config.genome_dir);
}
} else if(fstart == -1) {
fstart = i;
break;
Expand Down Expand Up @@ -216,6 +220,7 @@ int main(int argc, char *argv[]) {
}

//Close things up
if(config.genome_dir != NULL) free(config.genome_dir);
free(line);
free(chromosomes.genome);
for(i=0; i<chromosomes.nchromosomes; i++) {
Expand Down
9 changes: 7 additions & 2 deletions herd/main.c
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
#include <wordexp.h>

void usage(char *prog) {
printf("Usage: %s [OPTIONS] -g genome_dir {-1 fastq_A1.gz,fastq_B1.gz -2 fastq_A2.gz,fastq_B2.gz | -U fastq.gz}\n", prog);
printf("Usage: %s [OPTIONS] -g genome_dir/ {-1 fastq_A1.gz,fastq_B1.gz -2 fastq_A2.gz,fastq_B2.gz | -U fastq.gz}\n", prog);
printf("\n \
N.B., Bison has a number of defaults that are different from that of bowtie2.\n \
All of these can be changed with the normal bowtie2 options, which change\n \
Expand Down Expand Up @@ -162,6 +162,7 @@ int main(int argc, char *argv[]) {
config.n_compression_threads = 0;
config.unmapped1 = NULL;
config.unmapped2 = NULL;
config.genome_dir = NULL;
global_header = NULL;
unmapped1 = NULL;
unmapped2 = NULL;
Expand Down Expand Up @@ -215,7 +216,11 @@ int main(int argc, char *argv[]) {
config.FASTQ1 = argv[i];
} else if(strcmp(argv[i], "-g") == 0) {
i++;
config.genome_dir = argv[i];
config.genome_dir = strdup(argv[i]);
if(*(config.genome_dir+strlen(config.genome_dir)-1) != '/') {
config.genome_dir = realloc(config.genome_dir, sizeof(char) * (strlen(config.genome_dir)+2));
sprintf(config.genome_dir, "%s/", config.genome_dir);
}
} else if(strcmp(argv[i], "-p") == 0) {
i++;
config.nthreads = atoi(argv[i]);
Expand Down
8 changes: 7 additions & 1 deletion main.c
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Original file line number Diff line number Diff line change
Expand Up @@ -114,6 +114,7 @@ int main(int argc, char *argv[]) {
config.quiet = 0;
config.FASTQ1 = NULL;
config.FASTQ2 = NULL;
config.genome_dir = NULL;
chromosomes.max_genome = 3000000000;
chromosomes.nchromosomes = 0; //We need to initialize the struct

Expand Down Expand Up @@ -154,7 +155,11 @@ int main(int argc, char *argv[]) {
config.FASTQ1 = argv[i];
} else if(strcmp(argv[i], "-g") == 0) {
i++;
config.genome_dir = argv[i];
config.genome_dir = strdup(argv[i]);
if(*(config.genome_dir+strlen(config.genome_dir)-1) != '/') {
config.genome_dir = realloc(config.genome_dir, sizeof(char) * (strlen(config.genome_dir)+2));
sprintf(config.genome_dir, "%s/", config.genome_dir);
}
} else if(strcmp(argv[i], "-p") == 0) {
i++;
config.nthreads = atoi(argv[i]);
Expand Down Expand Up @@ -387,6 +392,7 @@ int main(int argc, char *argv[]) {

//Clean up
if(config.odir != NULL) free(config.odir);
if(config.genome_dir != NULL) free(config.genome_dir);
quit(3, 0);
return 0;
}
9 changes: 7 additions & 2 deletions methylation_extractor.c
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Original file line number Diff line number Diff line change
Expand Up @@ -769,7 +769,7 @@ void fill_bounds(char *str, int bounds[4]) {
}

void usage(char *prog) {
printf("Usage: %s [OPTIONS] genome_directory input.(sam|bam)\n", prog);
printf("Usage: %s [OPTIONS] genome_directory/ input.(sam|bam)\n", prog);
printf("\n\
Extract methylation information into a bedGraph file or files. By default,\n\
only CpG metrics are output\n\
Expand Down Expand Up @@ -883,7 +883,11 @@ int main(int argc, char *argv[]) {
} else if (strcmp(argv[i], "-CTOB") == 0) {
fill_bounds(argv[++i], CTOB);
} else if(config.genome_dir == NULL) {
config.genome_dir = argv[i];
config.genome_dir = strdup(argv[i]);
if(*(config.genome_dir+strlen(config.genome_dir)-1) != '/') {
config.genome_dir = realloc(config.genome_dir, sizeof(char) * (strlen(config.genome_dir)+2));
sprintf(config.genome_dir, "%s/", config.genome_dir);
}
} else if(strcmp(argv[i], "--genome-size") == 0) {
i++;
chromosomes.max_genome = strtoull(argv[i], NULL, 10);
Expand Down Expand Up @@ -1000,6 +1004,7 @@ int main(int argc, char *argv[]) {
free(*(chromosomes.chromosome+i));
}
free(chromosomes.chromosome);
if(config.genome_dir != NULL) free(config.genome_dir);
destroy_methyl_list(CpGlist);
destroy_methyl_list(CHGlist);
destroy_methyl_list(CHHlist);
Expand Down

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