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default output to STDOUT

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andrewjpage committed Jan 29, 2018
1 parent a323a50 commit a601b73cf11659cf363f024a00ae305e8fd4ec72
Showing with 13 additions and 11 deletions.
  1. +10 −8 README.md
  2. +1 −1 VERSION
  3. +2 −2 src/main.c
@@ -79,14 +79,16 @@ Bioconda produce a Docker container so you can use the software out of the box.
```
Usage: snp-sites [-mvph] [-o output_filename] <file>
This program finds snp sites from a multi fasta alignment file.
-r output internal pseudo reference sequence
-m output a multi fasta alignment file (default)
-v output a VCF file
-p output a phylip file
-o specify an output filename
-h this help message
-V print version and exit
<file> input alignment file which can optionally be gzipped
-r output internal pseudo reference sequence
-m output a multi fasta alignment file (default)
-v output a VCF file
-p output a phylip file
-o STR specify an output filename [STDOUT]
-c only output columns containing exclusively ACGT
-b output monomorphic sites, used for BEAST
-h this help message
-V print version and exit
<file> input alignment file which can optionally be gzipped
```

This application takes in a multi fasta alignment, finds all the SNP sites, then outputs the SNP sites in the following formats:
@@ -1 +1 @@
2.3.3
2.4.0
@@ -38,7 +38,7 @@ static void print_usage()
printf(" -m output a multi fasta alignment file (default)\n");
printf(" -v output a VCF file\n");
printf(" -p output a phylip file\n");
printf(" -o STR specify an output filename\n");
printf(" -o STR specify an output filename [STDOUT]\n");
printf(" -c only output columns containing exclusively ACGT\n");
printf(" -b output monomorphic sites, used for BEAST\n");
printf(" -h this help message\n");
@@ -62,7 +62,7 @@ static void print_version()

int main (int argc, char **argv) {
char multi_fasta_filename[FILENAME_MAX] = {""};
char output_filename[FILENAME_MAX] = {""};
char output_filename[FILENAME_MAX] = {"/dev/stdout"};

int c;
int index;

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