예제 #1
0
int main_flags(int argc, char *argv[])
{
    if ( argc!=2 ) usage();
    else
    {
        int mask = bam_str2flag(argv[1]);
        if ( mask<0 ) { fprintf(pysamerr,"Error: Could not parse \"%s\"\n", argv[1]); usage(); return 1; }
        printf("0x%x\t%d\t%s\n", mask, mask, bam_flag2str(mask));
    }
    return 0;
}
예제 #2
0
파일: mpileup.c 프로젝트: samtools/bcftools
static void print_usage(FILE *fp, const mplp_conf_t *mplp)
{
    char *tmp_require = bam_flag2str(mplp->rflag_require);
    char *tmp_filter  = bam_flag2str(mplp->rflag_filter);

    // Display usage information, formatted for the standard 80 columns.
    // (The unusual string formatting here aids the readability of this
    // source code in 80 columns, to the extent that's possible.)

    fprintf(fp,
"\n"
"Usage: bcftools mpileup [options] in1.bam [in2.bam [...]]\n"
"\n"
"Input options:\n"
"  -6, --illumina1.3+      quality is in the Illumina-1.3+ encoding\n"
"  -A, --count-orphans     do not discard anomalous read pairs\n"
"  -b, --bam-list FILE     list of input BAM filenames, one per line\n"
"  -B, --no-BAQ            disable BAQ (per-Base Alignment Quality)\n"
"  -C, --adjust-MQ INT     adjust mapping quality; recommended:50, disable:0 [0]\n"
"  -d, --max-depth INT     max per-file depth; avoids excessive memory usage [%d]\n", mplp->max_depth);
    fprintf(fp,
"  -E, --redo-BAQ          recalculate BAQ on the fly, ignore existing BQs\n"
"  -f, --fasta-ref FILE    faidx indexed reference sequence file\n"
"      --no-reference      do not require fasta reference file\n"
"  -G, --read-groups FILE  select or exclude read groups listed in the file\n"
"  -q, --min-MQ INT        skip alignments with mapQ smaller than INT [%d]\n", mplp->min_mq);
    fprintf(fp,
"  -Q, --min-BQ INT        skip bases with baseQ/BAQ smaller than INT [%d]\n", mplp->min_baseQ);
    fprintf(fp,
"  -r, --regions REG[,...] comma separated list of regions in which pileup is generated\n"
"  -R, --regions-file FILE restrict to regions listed in a file\n"
"      --ignore-RG         ignore RG tags (one BAM = one sample)\n"
"  --rf, --incl-flags STR|INT  required flags: skip reads with mask bits unset [%s]\n", tmp_require);
    fprintf(fp,
"  --ff, --excl-flags STR|INT  filter flags: skip reads with mask bits set\n"
"                                            [%s]\n", tmp_filter);
    fprintf(fp,
"  -s, --samples LIST      comma separated list of samples to include\n"
"  -S, --samples-file FILE file of samples to include\n"
"  -t, --targets REG[,...] similar to -r but streams rather than index-jumps\n"
"  -T, --targets-file FILE similar to -R but streams rather than index-jumps\n"
"  -x, --ignore-overlaps   disable read-pair overlap detection\n"
"\n"
"Output options:\n"
"  -a, --annotate LIST     optional tags to output; '?' to list []\n"
"  -g, --gvcf INT[,...]    group non-variant sites into gVCF blocks according\n"
"                          to minimum per-sample DP\n"
"      --no-version        do not append version and command line to the header\n"
"  -o, --output FILE       write output to FILE [standard output]\n"
"  -O, --output-type TYPE  'b' compressed BCF; 'u' uncompressed BCF;\n"
"                          'z' compressed VCF; 'v' uncompressed VCF [v]\n"
"      --threads INT       number of extra output compression threads [0]\n"
"\n"
"SNP/INDEL genotype likelihoods options:\n"
"  -e, --ext-prob INT      Phred-scaled gap extension seq error probability [%d]\n", mplp->extQ);
    fprintf(fp,
"  -F, --gap-frac FLOAT    minimum fraction of gapped reads [%g]\n", mplp->min_frac);
    fprintf(fp,
"  -h, --tandem-qual INT   coefficient for homopolymer errors [%d]\n", mplp->tandemQ);
    fprintf(fp,
"  -I, --skip-indels       do not perform indel calling\n"
"  -L, --max-idepth INT    maximum per-file depth for INDEL calling [%d]\n", mplp->max_indel_depth);
    fprintf(fp,
"  -m, --min-ireads INT    minimum number gapped reads for indel candidates [%d]\n", mplp->min_support);
    fprintf(fp,
"  -o, --open-prob INT     Phred-scaled gap open seq error probability [%d]\n", mplp->openQ);
    fprintf(fp,
"  -p, --per-sample-mF     apply -m and -F per-sample for increased sensitivity\n"
"  -P, --platforms STR     comma separated list of platforms for indels [all]\n"
"\n"
"Notes: Assuming diploid individuals.\n"
"\n");

    free(tmp_require);
    free(tmp_filter);
}
예제 #3
0
파일: bam_plcmd.c 프로젝트: Annak17/partis
static void print_usage(FILE *fp, const mplp_conf_t *mplp)
{
    char *tmp_require = bam_flag2str(mplp->rflag_require);
    char *tmp_filter  = bam_flag2str(mplp->rflag_filter);

    // Display usage information, formatted for the standard 80 columns.
    // (The unusual string formatting here aids the readability of this
    // source code in 80 columns, to the extent that's possible.)

    fprintf(fp,
"\n"
"Usage: samtools mpileup [options] in1.bam [in2.bam [...]]\n"
"\n"
"Input options:\n"
"  -6, --illumina1.3+      quality is in the Illumina-1.3+ encoding\n"
"  -A, --count-orphans     do not discard anomalous read pairs\n"
"  -b, --bam-list FILE     list of input BAM filenames, one per line\n"
"  -B, --no-BAQ            disable BAQ (per-Base Alignment Quality)\n"
"  -C, --adjust-MQ INT     adjust mapping quality; recommended:50, disable:0 [0]\n"
"  -d, --max-depth INT     max per-BAM depth; avoids excessive memory usage [%d]\n", mplp->max_depth);
    fprintf(fp,
"  -E, --redo-BAQ          recalculate BAQ on the fly, ignore existing BQs\n"
"  -f, --fasta-ref FILE    faidx indexed reference sequence file\n"
"  -G, --exclude-RG FILE   exclude read groups listed in FILE\n"
"  -l, --positions FILE    skip unlisted positions (chr pos) or regions (BED)\n"
"  -q, --min-MQ INT        skip alignments with mapQ smaller than INT [%d]\n", mplp->min_mq);
    fprintf(fp,
"  -Q, --min-BQ INT        skip bases with baseQ/BAQ smaller than INT [%d]\n", mplp->min_baseQ);
    fprintf(fp,
"  -r, --region REG        region in which pileup is generated\n"
"  -R, --ignore-RG         ignore RG tags (one BAM = one sample)\n"
"  --rf, --incl-flags STR|INT  required flags: skip reads with mask bits unset [%s]\n", tmp_require);
    fprintf(fp,
"  --ff, --excl-flags STR|INT  filter flags: skip reads with mask bits set\n"
"                                            [%s]\n", tmp_filter);
    fprintf(fp,
"  -x, --ignore-overlaps   disable read-pair overlap detection\n"
"\n"
"Output options:\n"
"  -o, --output FILE       write output to FILE [standard output]\n"
"  -g, --BCF               generate genotype likelihoods in BCF format\n"
"  -v, --VCF               generate genotype likelihoods in VCF format\n"
"\n"
"Output options for mpileup format (without -g/-v):\n"
"  -O, --output-BP         output base positions on reads\n"
"  -s, --output-MQ         output mapping quality\n"
"\n"
"Output options for genotype likelihoods (when -g/-v is used):\n"
"  -t, --output-tags LIST  optional tags to output: DP,DPR,DV,DP4,INFO/DPR,SP []\n"
"  -u, --uncompressed      generate uncompressed VCF/BCF output\n"
"\n"
"SNP/INDEL genotype likelihoods options (effective with -g/-v):\n"
"  -e, --ext-prob INT      Phred-scaled gap extension seq error probability [%d]\n", mplp->extQ);
    fprintf(fp,
"  -F, --gap-frac FLOAT    minimum fraction of gapped reads [%g]\n", mplp->min_frac);
    fprintf(fp,
"  -h, --tandem-qual INT   coefficient for homopolymer errors [%d]\n", mplp->tandemQ);
    fprintf(fp,
"  -I, --skip-indels       do not perform indel calling\n"
"  -L, --max-idepth INT    maximum per-sample depth for INDEL calling [%d]\n", mplp->max_indel_depth);
    fprintf(fp,
"  -m, --min-ireads INT    minimum number gapped reads for indel candidates [%d]\n", mplp->min_support);
    fprintf(fp,
"  -o, --open-prob INT     Phred-scaled gap open seq error probability [%d]\n", mplp->openQ);
    fprintf(fp,
"  -p, --per-sample-mF     apply -m and -F per-sample for increased sensitivity\n"
"  -P, --platforms STR     comma separated list of platforms for indels [all]\n"
"\n"
"Notes: Assuming diploid individuals.\n");

    free(tmp_require);
    free(tmp_filter);
}