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Searched refs:prev_chr (Results 1 – 21 of 21) sorted by relevance

/dports/science/dalton/dalton-66052b3af5ea7225e31178bf9a8b031913c72190/DALTON/fde/
H A Dxml_file.F90116 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
/dports/devel/vstr/vstr-1.0.15/examples/
H A Dex_ccount.c25 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()
/dports/biology/samtools/samtools-1.14/misc/
H A Dsam2vcf.pl126 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 = $chr;
H A Dplot-bamstats248 my ($prev_chr,$prev_pos);
256 if ( !defined $prev_chr or $chr ne $prev_chr ) { $prev_chr=$chr; $prev_pos=$from }
/dports/biology/seqan1/seqan-1.3.1/lib/samtools/misc/
H A Dsam2vcf.pl107 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 = $chr;
/dports/biology/vcftools/vcftools-0.1.16/src/perl/
H A Dvcf-fix-ploidy98 my ($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 = $$rec[0];
H A Dvcf-indel-stats76 my ($prev_chr,$prev_pos);
89 …if ( defined $prev_chr && $prev_chr eq $chr && $prev_pos>$pos ) { error("The VCF file must be sort…
90 $prev_chr = $chr;
H A Dvcf-isec358 my ($prev_chr,$prev_pos,$prev_id);
362 …elsif ( defined $prev_chr && $prev_chr eq $$rec{chr} && $prev_pos eq $$rec{pos} && $prev_id ne $$r…
383 $prev_chr = $$rec{chr};
H A Dvcf-phased-join103 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 = $chr;
H A Dvcf-annotate440 my ($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");
/dports/biology/hisat2/hisat2-2.2.1/
H A Dhisat2_extract_snps_haplotypes_UCSC.py349 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
H A Dhisat2_extract_snps_haplotypes_VCF.py615 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
/dports/audio/rhvoice/RHVoice-1.2.4/src/include/core/
H A Dstr.hpp468 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()
/dports/biology/bcftools/bcftools-1.14/
H A Dpolysomy.c202 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()
H A Dvcfconcat.c55 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()
/dports/biology/bio-mocha/bcftools-1.14/
H A Dpolysomy.c202 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()
H A Dvcfconcat.c55 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()
/dports/biology/py-pysam/pysam-0.18.0/bcftools/
H A Dvcfconcat.c55 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()
H A Dvcfconcat.c.pysam.c57 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()
/dports/biology/vcftools/vcftools-0.1.16/src/cpp/
H A Dvariant_file_output.cpp2983 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()
/dports/biology/plink/plink-ng-79b2df8c/2.0/
H A Dplink2_misc.cc772 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()