//read program parameters
void setArgsBam(argStruct *arguments){
int seed=0;
remove_bads = angsd::getArg("-remove_bads",remove_bads,arguments);
uniqueOnly = angsd::getArg("-uniqueOnly",uniqueOnly,arguments);
only_proper_pairs =angsd::getArg("-only_proper_pairs",only_proper_pairs,arguments);
fai_fname =angsd::getArg("-f",fai_fname,arguments);
minMapQ = angsd::getArg("-minMapQ",minMapQ,arguments);
cigstat = angsd::getArg("-cigstat",cigstat,arguments);
minQ = angsd::getArg("-minQ",minQ,arguments);
downSample = angsd::getArg("-downSample",downSample,arguments);
seed = angsd::getArg("-seed",seed,arguments);
trim = angsd::getArg("-trim",trim,arguments);
trim5 = angsd::getArg("-trim5",trim5,arguments);
trim3 = angsd::getArg("-trim3",trim3,arguments);
arguments->ref=angsd::getArg("-ref",arguments->ref,arguments);
arguments->anc=angsd::getArg("-anc",arguments->anc,arguments);
rghash_name= angsd::getArg("+RG",rghash_name,arguments);
if(rghash_name&&!angsd::fexists(rghash_name))
rghash = add_read_group_single(rghash_name);
if(rghash_name&&angsd::fexists(rghash_name))
rghash = add_read_groups_file(rghash_name);
if(rghash)
fprintf(stderr,"\t-> [READGROUP info] Number of readgroups to include: %d\n",khash_str2int_size(rghash));
adjustMapQ = angsd::getArg("-C",adjustMapQ,arguments);
baq = angsd::getArg("-baq",baq,arguments);
redo_baq = angsd::getArg("-redo-baq",redo_baq,arguments);
if(baq){
if(baq==1)
baq=1; //wauv
else if(baq==2)
baq=3;
else{
fprintf(stderr,"\t-> only supported options for -baq is: 1 (normal baq) and 2 (extended baq (SAMtools default)). Value supplied:%d\n",baq);
exit(0);//ly su
}
if(redo_baq==1)
baq |=4;
}
// fprintf(stderr,"baq:%d redobaq:%d\n",baq,redo_baq);exit(0);
regfile =angsd::getArg("-r",regfile,arguments);
regfiles = angsd::getArg("-rf",regfiles,arguments);
MAX_SEQ_LEN = angsd::getArg("-setMinChunkSize",MAX_SEQ_LEN,arguments);
checkBamHeaders = angsd::getArg("-checkBamHeaders",checkBamHeaders,arguments);
doCheck = angsd::getArg("-doCheck",doCheck,arguments);
MPLP_IGNORE_RG = angsd::getArg("--ignore-RG",MPLP_IGNORE_RG,arguments);
arguments->nReads = angsd::getArg("-nReads",arguments->nReads,arguments);
arguments->show = angsd::getArg("-show",arguments->show,arguments);
if(regfile && regfiles)
fprintf(stderr,"\t-> WARNING both -r and -rf has been set \n");
if(seed)
srand48(seed);
char *tmp = NULL;
tmp = angsd::getArg("-ref",tmp,arguments);
if(tmp==NULL && adjustMapQ!=0){
fprintf(stderr,"\t-> Must also supply -ref for adjusting the mapping quality\n");
exit(0);
}
if(tmp==NULL&&baq!=0){
fprintf(stderr,"\t-> Must also supply -ref for adjusting base qualities (baq)\n");
exit(0);
}
free(tmp);
std::vector<char *> regionsRaw;
if(regfiles)
regionsRaw = angsd::getFilenames(regfiles,0);
if(regfile)
regionsRaw.push_back(strdup(regfile));
// fprintf(stderr,"\t-> RegionsRaw.size():%lu hd:%p\n",regionsRaw.size(),arguments->hd);
for(size_t i=0;i<regionsRaw.size();i++){
regs tmpRegs;
if(parse_region(regionsRaw[i],arguments->hd,tmpRegs.refID,tmpRegs.start,tmpRegs.stop,arguments->revMap)<0||tmpRegs.stop<tmpRegs.start){
fprintf(stderr,"[%s] Problems with indexing: %s\n",__FUNCTION__,regionsRaw[i]);
exit(0);
}else
arguments->regions.push_back(tmpRegs);
free(regionsRaw[i]);
}
printArg(arguments->argumentFile,arguments);
if(regfile)
free(regfile);
if(regfiles)
free(regfiles);
}
int main_samview(int argc, char *argv[])
{
int index;
for(index = 0; index < argc; index++) {
printf("The %d is %s\n",index,argv[index]);
}
getchar();return 0;
int c, is_header = 0, is_header_only = 0, ret = 0, compress_level = -1, is_count = 0;
int is_long_help = 0, n_threads = 0;
int64_t count = 0;
samFile *in = 0, *out = 0, *un_out=0;
bam_hdr_t *header = NULL;
char out_mode[5], out_un_mode[5], *out_format = "";
char *fn_in = 0, *fn_out = 0, *fn_list = 0, *q, *fn_un_out = 0;
sam_global_args ga = SAM_GLOBAL_ARGS_INIT;
samview_settings_t settings = {
.rghash = NULL,
.min_mapQ = 0,
.flag_on = 0,
.flag_off = 0,
.min_qlen = 0,
.remove_B = 0,
.subsam_seed = 0,
.subsam_frac = -1.,
.library = NULL,
.bed = NULL,
};
static const struct option lopts[] = {
SAM_OPT_GLOBAL_OPTIONS('-', 0, 'O', 0, 'T'),
{ "threads", required_argument, NULL, '@' },
{ NULL, 0, NULL, 0 }
};
/* parse command-line options */
strcpy(out_mode, "w");
strcpy(out_un_mode, "w");
while ((c = getopt_long(argc, argv,
"SbBcCt:h1Ho:O:q:f:F:ul:r:?T:R:L:s:@:m:x:U:",
lopts, NULL)) >= 0) {
switch (c) {
case 's':
if ((settings.subsam_seed = strtol(optarg, &q, 10)) != 0) {
srand(settings.subsam_seed);
settings.subsam_seed = rand();
}
settings.subsam_frac = strtod(q, &q);
break;
case 'm': settings.min_qlen = atoi(optarg); break;
case 'c': is_count = 1; break;
case 'S': break;
case 'b': out_format = "b"; break;
case 'C': out_format = "c"; break;
case 't': fn_list = strdup(optarg); break;
case 'h': is_header = 1; break;
case 'H': is_header_only = 1; break;
case 'o': fn_out = strdup(optarg); break;
case 'U': fn_un_out = strdup(optarg); break;
case 'f': settings.flag_on |= strtol(optarg, 0, 0); break;
case 'F': settings.flag_off |= strtol(optarg, 0, 0); break;
case 'q': settings.min_mapQ = atoi(optarg); break;
case 'u': compress_level = 0; break;
case '1': compress_level = 1; break;
case 'l': settings.library = strdup(optarg); break;
case 'L':
if ((settings.bed = bed_read(optarg)) == NULL) {
print_error_errno("view", "Could not read file \"%s\"", optarg);
ret = 1;
goto view_end;
}
break;
case 'r':
if (add_read_group_single("view", &settings, optarg) != 0) {
ret = 1;
goto view_end;
}
break;
case 'R':
if (add_read_groups_file("view", &settings, optarg) != 0) {
ret = 1;
goto view_end;
}
break;
/* REMOVED as htslib doesn't support this
//case 'x': out_format = "x"; break;
//case 'X': out_format = "X"; break;
*/
case '?': is_long_help = 1; break;
case 'B': settings.remove_B = 1; break;
case '@': n_threads = strtol(optarg, 0, 0); break;
case 'x':
{
if (strlen(optarg) != 2) {
fprintf(stderr, "main_samview: Error parsing -x auxiliary tags should be exactly two characters long.\n");
return usage(stderr, EXIT_FAILURE, is_long_help);
}
settings.remove_aux = (char**)realloc(settings.remove_aux, sizeof(char*) * (++settings.remove_aux_len));
settings.remove_aux[settings.remove_aux_len-1] = optarg;
}
break;
default:
if (parse_sam_global_opt(c, optarg, lopts, &ga) != 0)
return usage(stderr, EXIT_FAILURE, is_long_help);
break;
}
}
if (compress_level >= 0 && !*out_format) out_format = "b";
if (is_header_only) is_header = 1;
// File format auto-detection first
if (fn_out) sam_open_mode(out_mode+1, fn_out, NULL);
if (fn_un_out) sam_open_mode(out_un_mode+1, fn_un_out, NULL);
// Overridden by manual -b, -C
if (*out_format)
out_mode[1] = out_un_mode[1] = *out_format;
out_mode[2] = out_un_mode[2] = '\0';
// out_(un_)mode now 1 or 2 bytes long, followed by nul.
if (compress_level >= 0) {
char tmp[2];
tmp[0] = compress_level + '0'; tmp[1] = '\0';
strcat(out_mode, tmp);
strcat(out_un_mode, tmp);
}
if (argc == optind && isatty(STDIN_FILENO)) return usage(stdout, EXIT_SUCCESS, is_long_help); // potential memory leak...
fn_in = (optind < argc)? argv[optind] : "-";
// generate the fn_list if necessary
if (fn_list == 0 && ga.reference) fn_list = samfaipath(ga.reference);
// open file handlers
if ((in = sam_open_format(fn_in, "r", &ga.in)) == 0) {
print_error_errno("view", "failed to open \"%s\" for reading", fn_in);
ret = 1;
goto view_end;
}
if (fn_list) {
if (hts_set_fai_filename(in, fn_list) != 0) {
fprintf(stderr, "[main_samview] failed to use reference \"%s\".\n", fn_list);
ret = 1;
goto view_end;
}
}
if ((header = sam_hdr_read(in)) == 0) {
fprintf(stderr, "[main_samview] fail to read the header from \"%s\".\n", fn_in);
ret = 1;
goto view_end;
}
if (settings.rghash) { // FIXME: I do not know what "bam_header_t::n_text" is for...
char *tmp;
int l;
tmp = drop_rg(header->text, settings.rghash, &l);
free(header->text);
header->text = tmp;
header->l_text = l;
}
if (!is_count) {
if ((out = sam_open_format(fn_out? fn_out : "-", out_mode, &ga.out)) == 0) {
print_error_errno("view", "failed to open \"%s\" for writing", fn_out? fn_out : "standard output");
ret = 1;
goto view_end;
}
if (fn_list) {
if (hts_set_fai_filename(out, fn_list) != 0) {
fprintf(stderr, "[main_samview] failed to use reference \"%s\".\n", fn_list);
ret = 1;
goto view_end;
}
}
if (*out_format || is_header ||
out_mode[1] == 'b' || out_mode[1] == 'c' ||
(ga.out.format != sam && ga.out.format != unknown_format)) {
if (sam_hdr_write(out, header) != 0) {
fprintf(stderr, "[main_samview] failed to write the SAM header\n");
ret = 1;
goto view_end;
}
}
if (fn_un_out) {
if ((un_out = sam_open_format(fn_un_out, out_un_mode, &ga.out)) == 0) {
print_error_errno("view", "failed to open \"%s\" for writing", fn_un_out);
ret = 1;
goto view_end;
}
if (fn_list) {
if (hts_set_fai_filename(un_out, fn_list) != 0) {
fprintf(stderr, "[main_samview] failed to use reference \"%s\".\n", fn_list);
ret = 1;
goto view_end;
}
}
if (*out_format || is_header ||
out_un_mode[1] == 'b' || out_un_mode[1] == 'c' ||
(ga.out.format != sam && ga.out.format != unknown_format)) {
if (sam_hdr_write(un_out, header) != 0) {
fprintf(stderr, "[main_samview] failed to write the SAM header\n");
ret = 1;
goto view_end;
}
}
}
}
if (n_threads > 1) { if (out) hts_set_threads(out, n_threads); }
if (is_header_only) goto view_end; // no need to print alignments
if (optind + 1 >= argc) { // convert/print the entire file
bam1_t *b = bam_init1();
int r;
while ((r = sam_read1(in, header, b)) >= 0) { // read one alignment from `in'
if (!process_aln(header, b, &settings)) {
if (!is_count) { if (check_sam_write1(out, header, b, fn_out, &ret) < 0) break; }
count++;
} else {
if (un_out) { if (check_sam_write1(un_out, header, b, fn_un_out, &ret) < 0) break; }
}
}
if (r < -1) {
fprintf(stderr, "[main_samview] truncated file.\n");
ret = 1;
}
bam_destroy1(b);
} else { // retrieve alignments in specified regions
int i;
bam1_t *b;
hts_idx_t *idx = sam_index_load(in, fn_in); // load index
if (idx == 0) { // index is unavailable
fprintf(stderr, "[main_samview] random alignment retrieval only works for indexed BAM or CRAM files.\n");
ret = 1;
goto view_end;
}
b = bam_init1();
for (i = optind + 1; i < argc; ++i) {
int result;
hts_itr_t *iter = sam_itr_querys(idx, header, argv[i]); // parse a region in the format like `chr2:100-200'
if (iter == NULL) { // region invalid or reference name not found
int beg, end;
if (hts_parse_reg(argv[i], &beg, &end))
fprintf(stderr, "[main_samview] region \"%s\" specifies an unknown reference name. Continue anyway.\n", argv[i]);
else
fprintf(stderr, "[main_samview] region \"%s\" could not be parsed. Continue anyway.\n", argv[i]);
continue;
}
// fetch alignments
while ((result = sam_itr_next(in, iter, b)) >= 0) {
if (!process_aln(header, b, &settings)) {
if (!is_count) { if (check_sam_write1(out, header, b, fn_out, &ret) < 0) break; }
count++;
} else {
if (un_out) { if (check_sam_write1(un_out, header, b, fn_un_out, &ret) < 0) break; }
}
}
hts_itr_destroy(iter);
if (result < -1) {
fprintf(stderr, "[main_samview] retrieval of region \"%s\" failed due to truncated file or corrupt BAM index file\n", argv[i]);
ret = 1;
break;
}
}
bam_destroy1(b);
hts_idx_destroy(idx); // destroy the BAM index
}
view_end:
if (is_count && ret == 0)
printf("%" PRId64 "\n", count);
// close files, free and return
if (in) check_sam_close("view", in, fn_in, "standard input", &ret);
if (out) check_sam_close("view", out, fn_out, "standard output", &ret);
if (un_out) check_sam_close("view", un_out, fn_un_out, "file", &ret);
free(fn_list); free(fn_out); free(settings.library); free(fn_un_out);
sam_global_args_free(&ga);
if ( header ) bam_hdr_destroy(header);
if (settings.bed) bed_destroy(settings.bed);
if (settings.rghash) {
khint_t k;
for (k = 0; k < kh_end(settings.rghash); ++k)
if (kh_exist(settings.rghash, k)) free((char*)kh_key(settings.rghash, k));
kh_destroy(rg, settings.rghash);
}
if (settings.remove_aux_len) {
free(settings.remove_aux);
}
return ret;
}
static int usage(FILE *fp, int exit_status, int is_long_help)
{
fprintf(fp,
"\n"
"Usage: samtools view [options] <in.bam>|<in.sam>|<in.cram> [region ...]\n"
"\n"
"Options:\n"
// output options
" -b output BAM\n"
" -C output CRAM (requires -T)\n"
" -1 use fast BAM compression (implies -b)\n"
" -u uncompressed BAM output (implies -b)\n"
" -h include header in SAM output\n"
" -H print SAM header only (no alignments)\n"
" -c print only the count of matching records\n"
" -o FILE output file name [stdout]\n"
" -U FILE output reads not selected by filters to FILE [null]\n"
// extra input
" -t FILE FILE listing reference names and lengths (see long help) [null]\n"
// read filters
" -L FILE only include reads overlapping this BED FILE [null]\n"
" -r STR only include reads in read group STR [null]\n"
" -R FILE only include reads with read group listed in FILE [null]\n"
" -q INT only include reads with mapping quality >= INT [0]\n"
" -l STR only include reads in library STR [null]\n"
" -m INT only include reads with number of CIGAR operations consuming\n"
" query sequence >= INT [0]\n"
" -f INT only include reads with all bits set in INT set in FLAG [0]\n"
" -F INT only include reads with none of the bits set in INT set in FLAG [0]\n"
// read processing
" -x STR read tag to strip (repeatable) [null]\n"
" -B collapse the backward CIGAR operation\n"
" -s FLOAT integer part sets seed of random number generator [0];\n"
" rest sets fraction of templates to subsample [no subsampling]\n"
// general options
" -@, --threads INT\n"
" number of BAM/CRAM compression threads [0]\n"
" -? print long help, including note about region specification\n"
" -S ignored (input format is auto-detected)\n");
sam_global_opt_help(fp, "-.O.T");
fprintf(fp, "\n");
if (is_long_help)
fprintf(fp,
"Notes:\n"
"\n"
"1. This command now auto-detects the input format (BAM/CRAM/SAM).\n"
" Further control over the CRAM format can be specified by using the\n"
" --output-fmt-option, e.g. to specify the number of sequences per slice\n"
" and to use avoid reference based compression:\n"
"\n"
"\tsamtools view -C --output-fmt-option seqs_per_slice=5000 \\\n"
"\t --output-fmt-option no_ref -o out.cram in.bam\n"
"\n"
" Options can also be specified as a comma separated list within the\n"
" --output-fmt value too. For example this is equivalent to the above\n"
"\n"
"\tsamtools view --output-fmt cram,seqs_per_slice=5000,no_ref \\\n"
"\t -o out.cram in.bam\n"
"\n"
"2. The file supplied with `-t' is SPACE/TAB delimited with the first\n"
" two fields of each line consisting of the reference name and the\n"
" corresponding sequence length. The `.fai' file generated by \n"
" `samtools faidx' is suitable for use as this file. This may be an\n"
" empty file if reads are unaligned.\n"
"\n"
"3. SAM->BAM conversion: samtools view -bT ref.fa in.sam.gz\n"
"\n"
"4. BAM->SAM conversion: samtools view -h in.bam\n"
"\n"
"5. A region should be presented in one of the following formats:\n"
" `chr1', `chr2:1,000' and `chr3:1000-2,000'. When a region is\n"
" specified, the input alignment file must be a sorted and indexed\n"
" alignment (BAM/CRAM) file.\n"
"\n"
"6. Option `-u' is preferred over `-b' when the output is piped to\n"
" another samtools command.\n"
"\n");
return exit_status;
}