/dports/science/dalton/dalton-66052b3af5ea7225e31178bf9a8b031913c72190/DALTON/fde/ |
H A D | xml_file.F90 | 116 character(len=1) :: chr,prev_chr local 122 select case(prev_chr) 124 var=prev_chr 125 prev_chr='' 128 prev_chr='' 138 prev_chr=chr
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/dports/devel/vstr/vstr-1.0.15/examples/ |
H A D | ex_ccount.c | 25 static char prev_chr = 0; in ex_ccount_process() local 32 prnt_chrs(s1, prev_chr, &prev_len); in ex_ccount_process() 41 if (prev_len && (chrs[0] != prev_chr)) in ex_ccount_process() 42 prnt_chrs(s1, prev_chr, &prev_len); in ex_ccount_process() 52 prev_chr = chrs[0]; in ex_ccount_process() 57 prnt_chrs(s1, prev_chr, &prev_len); in ex_ccount_process()
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/dports/biology/samtools/samtools-1.14/misc/ |
H A D | sam2vcf.pl | 126 my ($prev_chr,$prev_pos,$prev_ref); 162 $prev_chr = $chr; 166 if (!defined $prev_chr || $chr ne $prev_chr || $pos ne $prev_pos) 209 $prev_chr = $chr; 221 $prev_chr = $chr;
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H A D | plot-bamstats | 248 my ($prev_chr,$prev_pos); 256 if ( !defined $prev_chr or $chr ne $prev_chr ) { $prev_chr=$chr; $prev_pos=$from }
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/dports/biology/seqan1/seqan-1.3.1/lib/samtools/misc/ |
H A D | sam2vcf.pl | 107 my ($prev_chr,$prev_pos,$prev_ref); 143 $prev_chr = $chr; 147 if (!defined $prev_chr || $chr ne $prev_chr || $pos ne $prev_pos) 190 $prev_chr = $chr; 202 $prev_chr = $chr;
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/dports/biology/vcftools/vcftools-0.1.16/src/perl/ |
H A D | vcf-fix-ploidy | 98 my ($prev_chr,$prev_pos,$regions,$iregion,$nregions); 103 if ( !defined $prev_chr or $$rec[0] ne $prev_chr ) 105 $prev_chr = $$rec[0]; 107 if ( exists($$opts{regions}{$prev_chr}) ) 109 $regions = $$opts{regions}{$prev_chr}; 118 $prev_chr = $$rec[0];
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H A D | vcf-indel-stats | 76 my ($prev_chr,$prev_pos); 89 …if ( defined $prev_chr && $prev_chr eq $chr && $prev_pos>$pos ) { error("The VCF file must be sort… 90 $prev_chr = $chr;
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H A D | vcf-isec | 358 my ($prev_chr,$prev_pos,$prev_id); 362 …elsif ( defined $prev_chr && $prev_chr eq $$rec{chr} && $prev_pos eq $$rec{pos} && $prev_id ne $$r… 383 $prev_chr = $$rec{chr};
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H A D | vcf-phased-join | 103 my ($fh,$prev_boundary,$start_pos,@buffer,$prev_chr,$prev_pos,$swap); 111 if ( defined $prev_chr && $prev_chr ne $chr ) { last; } 114 $prev_chr = $chr;
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H A D | vcf-annotate | 440 my ($prev_chr,$prev_pos,$annot_from,$annot_to,$annot_line); 464 $prev_chr = $rec[0]; 467 $reader->open(region=>"$prev_chr:$prev_pos"); 513 if ( $chr ne $prev_chr ) 516 $prev_chr = $chr; 518 $reader->open(region=>"$prev_chr:$prev_pos");
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/dports/biology/hisat2/hisat2-2.2.1/ |
H A D | hisat2_extract_snps_haplotypes_UCSC.py | 349 prev_chr, curr_right = "", -1 413 if (prev_chr != chr or curr_right + inter_gap < start) and \ 510 if prev_chr != chr: 512 prev_chr = chr
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H A D | hisat2_extract_snps_haplotypes_VCF.py | 615 prev_varID, prev_chr, prev_pos = "", "", -1 625 if prev_chr != chr: 700 (curr_right + inter_gap < pos or prev_chr != chr): 765 prev_chr = chr
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/dports/audio/rhvoice/RHVoice-1.2.4/src/include/core/ |
H A D | str.hpp | 468 utf8::uint32_t prev_chr=0; in count_newlines() local 473 … if(((chr=='\n')&&(prev_chr!='\r'))||(chr=='\r')||(chr==0x85)||(chr==0x2028)||(chr==0x2029)) in count_newlines() 475 prev_chr=chr; in count_newlines()
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/dports/biology/bcftools/bcftools-1.14/ |
H A D | polysomy.c | 202 int idist = -1, nbaf = 0, nprocessed = 0, ntotal = 0, prev_chr = -1; in init_data() local 214 if ( prev_chr==-1 || prev_chr!=line->rid ) in init_data() 224 prev_chr = line->rid; in init_data()
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H A D | vcfconcat.c | 55 int nbuf, mbuf, prev_chr, min_PQ, prev_pos_check; member 191 args->prev_chr = -1; in init_data() 396 if ( args->prev_chr<0 || args->prev_chr!=chr_id ) in phased_push() 398 if ( args->prev_chr>=0 ) phased_flush(args); in phased_push() 406 args->prev_chr = chr_id; in phased_push()
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/dports/biology/bio-mocha/bcftools-1.14/ |
H A D | polysomy.c | 202 int idist = -1, nbaf = 0, nprocessed = 0, ntotal = 0, prev_chr = -1; in init_data() local 214 if ( prev_chr==-1 || prev_chr!=line->rid ) in init_data() 224 prev_chr = line->rid; in init_data()
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H A D | vcfconcat.c | 55 int nbuf, mbuf, prev_chr, min_PQ, prev_pos_check; member 191 args->prev_chr = -1; in init_data() 396 if ( args->prev_chr<0 || args->prev_chr!=chr_id ) in phased_push() 398 if ( args->prev_chr>=0 ) phased_flush(args); in phased_push() 406 args->prev_chr = chr_id; in phased_push()
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/dports/biology/py-pysam/pysam-0.18.0/bcftools/ |
H A D | vcfconcat.c | 55 int nbuf, mbuf, prev_chr, min_PQ, prev_pos_check; member 191 args->prev_chr = -1; in init_data() 396 if ( args->prev_chr<0 || args->prev_chr!=chr_id ) in phased_push() 398 if ( args->prev_chr>=0 ) phased_flush(args); in phased_push() 406 args->prev_chr = chr_id; in phased_push()
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H A D | vcfconcat.c.pysam.c | 57 int nbuf, mbuf, prev_chr, min_PQ, prev_pos_check; member 193 args->prev_chr = -1; in init_data() 398 if ( args->prev_chr<0 || args->prev_chr!=chr_id ) in phased_push() 400 if ( args->prev_chr>=0 ) phased_flush(args); in phased_push() 408 args->prev_chr = chr_id; in phased_push()
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/dports/biology/vcftools/vcftools-0.1.16/src/cpp/ |
H A D | variant_file_output.cpp | 2983 string prev_chr = ""; in output_TsTv() local 3014 if(CHROM != prev_chr) in output_TsTv() 3017 prev_chr = CHROM; in output_TsTv() 3980 string prev_chr = ""; in output_Tajima_D() local 4016 if(CHROM != prev_chr) in output_Tajima_D() 4019 prev_chr = CHROM; in output_Tajima_D() 4101 string prev_chr; in output_windowed_nucleotide_diversity() local 4146 if(CHROM != prev_chr) in output_windowed_nucleotide_diversity() 4149 prev_chr = CHROM; in output_windowed_nucleotide_diversity()
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/dports/biology/plink/plink-ng-79b2df8c/2.0/ |
H A D | plink2_misc.cc | 772 uint32_t prev_chr = UINT32_MAX; in RecoverVarIds() local 803 if (cur_chr_code == prev_chr) { in RecoverVarIds() 808 prev_chr = cur_chr_code; in RecoverVarIds()
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