From 55f436ab58ee5270fa9cb5a6cb9809d5c40cfe7a Mon Sep 17 00:00:00 2001 From: Calvin Date: Mon, 20 May 2013 15:15:39 -0400 Subject: updated documentation strings, add man page to be installed globally --- Makefile | 3 +++ src/c/multifasta_to_otu.c | 2 +- src/c/quikr.c | 6 +++--- src/c/quikr_train.c | 2 +- 4 files changed, 8 insertions(+), 5 deletions(-) diff --git a/Makefile b/Makefile index 166255c..ec7a78c 100644 --- a/Makefile +++ b/Makefile @@ -16,6 +16,9 @@ install: chmod -v 755 ${DESTDIR}${PREFIX}/bin/quikr_train chmod -v 755 ${DESTDIR}${PREFIX}/bin/multifasta_to_otu chmod -v 755 ${DESTDIR}${PREFIX}/bin/generate_kmers + @cp -vf src/c/quikr.1 ${DESTDIR}${PREFIX}/share/man/man1/quikr.1 + @cp -vf src/c/quikr_train.1 ${DESTDIR}${PREFIX}/share/man/man1/quikr_train.1 + @cp -vf src/c/multifasta_to_otu.1 ${DESTDIR}${PREFIX}/share/man/man1/multifasta_to_otu.1 nbc: @echo "building nbc" diff --git a/src/c/multifasta_to_otu.c b/src/c/multifasta_to_otu.c index f61c76f..0d81e13 100644 --- a/src/c/multifasta_to_otu.c +++ b/src/c/multifasta_to_otu.c @@ -112,7 +112,7 @@ int main(int argc, char **argv) { exit(EXIT_FAILURE); } if(output_filename == NULL) { - fprintf(stderr, "Error: Output Filename (-o) must be specified\n\n"); + fprintf(stderr, "Error: output filename (-o) must be specified\n\n"); fprintf(stderr, "%s\n", USAGE); exit(EXIT_FAILURE); } diff --git a/src/c/quikr.c b/src/c/quikr.c index e0ba77e..123756c 100644 --- a/src/c/quikr.c +++ b/src/c/quikr.c @@ -12,7 +12,7 @@ #include "quikr_functions.h" #define sensing_matrix(i,j) (sensing_matrix[width*i + j]) -#define USAGE "Usage:\n\tmultifasta_to_otu [OPTION...] - Calculate estimated frequencies of bacteria in a sample.\n\nOptions:\n\n-i, --input\n\tthe sample's fasta file of NGS READS (fasta format)\n\n-f, --sensing-fasta\n\tlocation of the fasta file database used to create the sensing matrix (fasta format)\n\n-s, --sensing-matrix\n\t location of the sensing matrix. (trained from quikr_train)\n\n-k, --kmer\n\tspecify what size of kmer to use. (default value is 6)\n\n-l, --lambda\n\tlambda value to use. (default value is 10000)\n\n-o, --output\n\tthe sensing matrix. (a gzip'd text file)\n\n-v, --verbose\n\tverbose mode.\n\n-d, --debug\n\tdebug mode, this will save our sensing matrix and sample matrix (A and B matricies) in files called 'sensing.matrix' and 'count.matrix' for debugging purposes" +#define USAGE "Usage:\n\tmultifasta_to_otu [OPTION...] - Calculate estimated frequencies of bacteria in a sample.\n\nOptions:\n\n-i, --input\n\tthe sample's fasta file of NGS READS (fasta format)\n\n-f, --sensing-fasta\n\tlocation of the fasta file database used to create the sensing matrix (fasta format)\n\n-s, --sensing-matrix\n\t location of the sensing matrix. (trained from quikr_train)\n\n-k, --kmer\n\tspecify what size of kmer to use. (default value is 6)\n\n-l, --lambda\n\tlambda value to use. (default value is 10000)\n\n-o, --output\n\tthe sensing matrix. (a gzip'd text file)\n\n-v, --verbose\n\tverbose mode.\n\n-d, --debug\n\tdebug mode, read manpage for more details" int main(int argc, char **argv) { @@ -97,12 +97,12 @@ int main(int argc, char **argv) { exit(EXIT_FAILURE); } if(sensing_fasta_filename == NULL) { - fprintf(stderr, "Error: sensing matrix filename (-f) must be specified\n\n"); + fprintf(stderr, "Error: sensing fasta filename (-f) must be specified\n\n"); fprintf(stderr, "%s\n", USAGE); exit(EXIT_FAILURE); } if(output_filename == NULL) { - fprintf(stderr, "Error: Output Filename (-o) must be specified\n\n"); + fprintf(stderr, "Error: output filename (-o) must be specified\n\n"); fprintf(stderr, "%s\n", USAGE); exit(EXIT_FAILURE); } diff --git a/src/c/quikr_train.c b/src/c/quikr_train.c index 1585629..86bd77e 100644 --- a/src/c/quikr_train.c +++ b/src/c/quikr_train.c @@ -83,7 +83,7 @@ int main(int argc, char **argv) { } if(output_file == NULL) { - fprintf(stderr, "Error: output directory (-o) must be specified\n\n"); + fprintf(stderr, "Error: output matrix file (-o) must be specified\n\n"); fprintf(stderr, "%s\n", USAGE); exit(EXIT_FAILURE); } -- cgit v1.2.3