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/dports/games/scummvm/scummvm-2.5.1/engines/ultima/nuvie/sound/decoder/
H A Dfm_towns_decoder_stream.cpp41 U6Lib_n sam_file; in FMtownsDecoderStream() local
44 sam_file.open(filename, 4); in FMtownsDecoderStream()
46 item_data = sam_file.get_item(sample_num, NULL); in FMtownsDecoderStream()
49 raw_audio_buf = lzw.decompress_buffer(item_data, sam_file.get_item_size(sample_num), decomp_size); in FMtownsDecoderStream()
56 buf_len = sam_file.get_item_size(sample_num); in FMtownsDecoderStream()
/dports/biology/samtools/samtools-1.14/misc/
H A Dinterpolate_sam.pl43 my $sam_file = $ARGV[0];
44 if(!defined($sam_file)) { die("No sam file defined on arg 1"); }
45 unless(-f $sam_file) { die("Sam file does not exist: $sam_file"); }
46 open(SAM, $sam_file) || die("Cannot open sam file");
/dports/biology/seqan1/seqan-1.3.1/lib/samtools/misc/
H A Dinterpolate_sam.pl19 my $sam_file = $ARGV[0];
20 if(!defined($sam_file)) { die("No sam file defined on arg 1"); }
21 unless(-f $sam_file) { die("Sam file does not exist: $sam_file"); }
22 open(SAM, $sam_file) || die("Cannot open sam file");
/dports/games/scummvm/scummvm-2.5.1/engines/ultima/nuvie/core/
H A Dconverse_speech.cpp110 U6Lib_n sam_file; in load_speech() local
115 sam_file.open(filename, 4); in load_speech()
117 compressed_data = sam_file.get_item(sample_num, NULL); in load_speech()
118 …raw_audio = lzw.decompress_buffer(compressed_data, sam_file.get_item_size(sample_num), decomp_size… in load_speech()
/dports/biology/py-hits/hits-0.1/hits/
H A Dmapping_tools.py36 with open(sam_file_name, 'w') as sam_file, open(error_file_name, 'a') as error_file:
44 stdout=sam_file,
78 with open(sam_file_name, 'w') as sam_file, open(error_file_name, 'a') as error_file:
80 stdout=sam_file,
362 sam_file = pysam.AlignmentFile(str(output_file_name), 'r')
363 yield sam_file
364 for read in sam_file:
424 sam_file = next(generator)
425 return sam_file, generator
H A Dvariants.py214 def count_pe_mismatches(sam_file, argument
261 rname = sam_file.getrname(mapping.tid)
508 sam_file=bam_file,
H A Dsam.py797 sam_file = pysam.AlignmentFile(str(sam_file_name))
798 for mapping in sam_file:
842 self.sam_file = pysam.AlignmentFile(self.fifo.file_name, 'wbu', header=self.header)
847 self.sam_file.close()
861 self.sam_file.write(alignment)
H A Dvisualize_structure.py66 sam_file, mappings = mapping_tools.map_bowtie2(index_prefix,
/dports/biology/hisat2/hisat2-2.2.1/evaluation/tests/one_snp_test/
H A Dsimulate_one_snp_reads.py277 sam_file = open(base_fname + ".sam", "w")
280 print >> sam_file, "@HD\tVN:1.0\tSO:unsorted"
282 print >> sam_file, "@SQ\tSN:%s\tLN:%d" % (chr, len(genome_seq[chr]))
317 …print >> sam_file, "{}\t{}\t{}\t{}\t255\t{}\t{}\t{}\t0\t{}\t*\tXM:i:0\tNM:i:0\tMD:Z:{}{}".format(r…
330 sam_file.close()
/dports/biology/hisat2/hisat2-2.2.1/evaluation/simulation/
H A Dinit.py163 sam_file = open("sim_paired.sam")
165 sam_file = open("sim_1.sam")
247 for line in sam_file:
270 sam_file.close()
/dports/net/samba412/samba-4.12.15/python/samba/netcmd/
H A Ddomain_backup.py982 for sam_file in os.listdir(sam_ldb_d):
983 sam_file = os.path.join(sam_ldb_d, sam_file)
984 if sam_file.endswith('.ldb'):
985 logger.info(' backing up locked/related file ' + sam_file)
986 copy_function(sam_file)
988 logger.info(' copying locked/related file ' + sam_file)
989 shutil.copyfile(sam_file, sam_file + self.backup_ext)
/dports/biology/bedtools/bedtools2-2.30.0/src/utils/BamTools/include/
H A DBamReader.hpp178 _SamFile* sam_file = new _SamFile(fp, idx, this); in _Open_impl() local
187 sam_file->set_cram_reqd_fields(2559); in _Open_impl()
196 _files.push_back(sam_file); in _Open_impl()
/dports/biology/hisat2/hisat2-2.2.1/
H A Dhisat2_simulate_reads.py747 sam_file = open(base_fname + ".sam", "w")
750 print("@HD\tVN:1.0\tSO:unsorted", file=sam_file)
752 print("@SQ\tSN:%s\tLN:%d" % (chr, len(genome_seq[chr])), file=sam_file)
850 …id, flag, chr, pos + 1, cigar_str, chr, pos2 + 1, read_seq, XM, NM, MD, Zs, XS, TI), file=sam_file)
857 …g2, chr, pos2 + 1, cigar2_str, chr, pos + 1, read2_seq, XM2, NM2, MD2, Zs2, XS, TI), file=sam_file)
861 sam_file.close()
/dports/biology/bcftools/bcftools-1.14/test/mpileup/
H A Dmpileup.1.sam58 @PG ID:bwa_sam PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1350 -r $rg_line -f $sam_file $…
59 @PG ID:bwa_sam.1 PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1056 -r $rg_line -f $sam_file…
60 @PG ID:bwa_sam.2 PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1047 -r $rg_line -f $sam_file…
61 @PG ID:bwa_sam.3 PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1044 -r $rg_line -f $sam_file…
62 @PG ID:bwa_sam.4 PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1377 -r $rg_line -f $sam_file…
63 @PG ID:bwa_sam.5 PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1371 -r $rg_line -f $sam_file…
64 @PG ID:bwa_sam.6 PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1368 -r $rg_line -f $sam_file…
65 @PG ID:bwa_sam.7 PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1371 -r $rg_line -f $sam_file…
66 @PG ID:bwa_sam.8 PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1374 -r $rg_line -f $sam_file…
67 @PG ID:bwa_sam.9 PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1371 -r $rg_line -f $sam_file…
[all …]
H A Dmpileup.3.sam6 @PG ID:bwa_sam PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1491 -r $rg_line -f $sam_file $…
7 @PG ID:sam_to_fixed_bam PN:samtools PP:bwa_sam VN:0.1.17 (r973:277) CL:samtools view -bSu $sam_file…
/dports/biology/bio-mocha/bcftools-1.14/test/mpileup/
H A Dmpileup.1.sam58 @PG ID:bwa_sam PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1350 -r $rg_line -f $sam_file $…
59 @PG ID:bwa_sam.1 PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1056 -r $rg_line -f $sam_file…
60 @PG ID:bwa_sam.2 PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1047 -r $rg_line -f $sam_file…
61 @PG ID:bwa_sam.3 PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1044 -r $rg_line -f $sam_file…
62 @PG ID:bwa_sam.4 PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1377 -r $rg_line -f $sam_file…
63 @PG ID:bwa_sam.5 PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1371 -r $rg_line -f $sam_file…
64 @PG ID:bwa_sam.6 PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1368 -r $rg_line -f $sam_file…
65 @PG ID:bwa_sam.7 PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1371 -r $rg_line -f $sam_file…
66 @PG ID:bwa_sam.8 PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1374 -r $rg_line -f $sam_file…
67 @PG ID:bwa_sam.9 PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1371 -r $rg_line -f $sam_file…
[all …]
H A Dmpileup.3.sam6 @PG ID:bwa_sam PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1491 -r $rg_line -f $sam_file $…
7 @PG ID:sam_to_fixed_bam PN:samtools PP:bwa_sam VN:0.1.17 (r973:277) CL:samtools view -bSu $sam_file…
/dports/biology/samtools/samtools-1.14/test/dat/
H A Dmpileup.1.sam58 @PG ID:bwa_sam PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1350 -r $rg_line -f $sam_file $…
59 @PG ID:bwa_sam.1 PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1056 -r $rg_line -f $sam_file…
60 @PG ID:bwa_sam.2 PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1047 -r $rg_line -f $sam_file…
61 @PG ID:bwa_sam.3 PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1044 -r $rg_line -f $sam_file…
62 @PG ID:bwa_sam.4 PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1377 -r $rg_line -f $sam_file…
63 @PG ID:bwa_sam.5 PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1371 -r $rg_line -f $sam_file…
64 @PG ID:bwa_sam.6 PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1368 -r $rg_line -f $sam_file…
65 @PG ID:bwa_sam.7 PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1371 -r $rg_line -f $sam_file…
66 @PG ID:bwa_sam.8 PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1374 -r $rg_line -f $sam_file…
67 @PG ID:bwa_sam.9 PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1371 -r $rg_line -f $sam_file…
[all …]
H A Dmpileup.3.sam6 @PG ID:bwa_sam PN:bwa PP:bwa_aln_fastq VN:0.5.9-r16 CL:bwa sampe -a 1491 -r $rg_line -f $sam_file $…
7 @PG ID:sam_to_fixed_bam PN:samtools PP:bwa_sam VN:0.1.17 (r973:277) CL:samtools view -bSu $sam_file…
/dports/audio/snd/snd-21.2/tools/
H A Dsam.c2798 FILE *sam_file; in main() local
2801 sam_file = fopen(filename, "r"); in main()
2802 if (!sam_file) in main()
2807 fseek(sam_file, 0, SEEK_END); in main()
2808 size = ftell(sam_file); in main()
2809 rewind(sam_file); in main()
2814 fclose(sam_file); in main()
2835 bytes = fread(command, sizeof(unsigned char), size, sam_file); in main()
2836 fclose(sam_file); in main()
/dports/biology/cufflinks/cufflinks-2.2.1-89-gdc3b0cb/src/
H A Dcuffmerge164 sam_file,
191 cmd.append(sam_file)
H A Dcuffnorm.cpp456 string sam_file = columns[0]; in parse_sample_sheet_file() local
460 inserted.first->second.push_back(sam_file); in parse_sample_sheet_file()
H A Dcuffdiff.cpp1163 string sam_file = columns[0]; in parse_sample_sheet_file() local
1167 inserted.first->second.push_back(sam_file); in parse_sample_sheet_file()
/dports/biology/samtools/samtools-1.14/test/
H A Dtest.pl2167 my $sam_file = "$$opts{tmp}/view.001.$$filter[0].sam";
2168 filter_sam($sam_with_ur, $sam_file, $$filter[1]);
2177 compare => $sam_file,
2187 compare_count => $sam_file,
2303 my $sam_file = "$$opts{tmp}/view.$$rt[0].sam";
2304 filter_sam($input_sam, $sam_file, $$rt[2]);
2313 compare => $sam_file);
2321 compare_count => $sam_file);
/dports/biology/hisat2/hisat2-2.2.1/evaluation/real/
H A Dcalculate_read_cost.py472 sam_file = open(sam_filename, "r")
473 for line in sam_file:
625 sam_file.close()

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