| /dports/biology/gatk/gatk-4.2.0.0/src/main/python/org/broadinstitute/hellbender/gcnvkernel/io/ |
| H A D | io_metadata.py | 35 …contig_list = sample_metadata_collection.sample_coverage_metadata_dict[sample_names[0]].contig_list
37 …rt sample_metadata_collection.sample_coverage_metadata_dict[sample_name].contig_list == contig_list
42 header = [io_consts.sample_name_column_name] + [contig for contig in contig_list]
46 … row = ([sample_name] + [repr(sample_coverage_metadata.n_j[j]) for j in range(len(contig_list))])
69 contig_list = [str(column_name) for column_name in coverage_metadata_pd.columns]
70 contig_list.remove(io_consts.sample_name_column_name)
71 num_contigs = len(contig_list)
74 *(coverage_metadata_pd[contig] for contig in contig_list)):
78 sample_name, n_j, contig_list))
133 contig_list = sample_ploidy_pd[io_consts.contig_column_name].values
[all …]
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| H A D | io_ploidy.py | 91 for j, contig in enumerate(sample_ploidy_metadata.contig_list):
192 contig_list = [str(x) for x in contig_ploidy_prior_pd['CONTIG_NAME'].values]
199 for contig in contig_list:
205 for j, contig in enumerate(contig_list):
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/python/org/broadinstitute/hellbender/gcnvkernel/structs/ |
| H A D | metadata.py | 52 contig_list: List[str]):
54 assert n_j.size == len(contig_list)
57 self.contig_list = contig_list
64 self._contig_map = {contig: j for j, contig in enumerate(contig_list)}
95 contig_list: List[str],
98 assert ploidy_j.size == len(contig_list)
100 assert ploidy_genotyping_quality_j.size == len(contig_list)
103 self.contig_list = contig_list
106 self._contig_map = {contig: j for j, contig in enumerate(contig_list)}
143 for j, contig in enumerate(self.contig_list):
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/python/org/broadinstitute/hellbender/gcnvkernel/models/ |
| H A D | model_denoising_calling.py | 371 self.contig_list = list({interval.contig for interval in interval_list})
372 self.num_contigs = len(self.contig_list)
373 contig_to_j_map = {contig: self.contig_list.index(contig) for contig in self.contig_list}
381 sample_metadata_collection, sample_names, self.contig_list)
610 contig_list: List[str]) \
629 num_contigs = len(contig_list)
642 … for contig in contig_list], dtype=types.small_uint)
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| /dports/biology/ncbi-toolkit/ncbi/desktop/ |
| H A D | mapgene.h | 79 Boolean PrintContigForOneMap PROTO((SeqIdPtr chr_id, ValNodePtr contig_list,
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| H A D | drawseq.h | 326 void AddIntervalForImage PROTO((ValNodePtr contig_list, ValNodePtr image_list));
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| H A D | mapgene.c | 3396 Boolean PrintContigForOneMap(SeqIdPtr chr_id, ValNodePtr contig_list, in PrintContigForOneMap() argument
3400 if(contig_list == NULL || fp == NULL) in PrintContigForOneMap()
3410 return print_contig_info (contig_list, band_name, chr_id, include_amb, fp); in PrintContigForOneMap()
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| H A D | drawseq.c | 4517 void AddIntervalForImage(ValNodePtr contig_list, ValNodePtr image_list) in AddIntervalForImage() argument
4528 for(vnp = contig_list; vnp != NULL; vnp = vnp->next) in AddIntervalForImage()
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| /dports/biology/ncbi-toolkit/ncbi/api/ |
| H A D | aceread.c | 2341 static TACEFilePtr ACEFileFromConsensusReadsList (TConsensusReadsListPtr contig_list) in ACEFileFromConsensusReadsList() argument
2347 if (contig_list == NULL || contig_list->num_contigs == 0) { in ACEFileFromConsensusReadsList()
2352 for (c = contig_list; c != NULL; c=c->next) { in ACEFileFromConsensusReadsList()
2357 for (c = contig_list; c != NULL; c = c->next) { in ACEFileFromConsensusReadsList()
2381 TConsensusReadsListPtr contig_list = NULL, contig_last = NULL; in ReadAssemblyFile() local
2397 if (contig_list == NULL) { in ReadAssemblyFile()
2398 contig_list = contig_last; in ReadAssemblyFile()
2411 afp = ACEFileFromConsensusReadsList (contig_list); in ReadAssemblyFile()
2412 contig_list = ConsensusReadsListFree (contig_list); in ReadAssemblyFile()
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| H A D | maputil.c | 2579 ValNodePtr list, curr, contig_list; in MapContigPosition() local
2642 contig_list = NULL; in MapContigPosition()
2647 ValNodeAddPointer(&contig_list, 0, cmp->slp); in MapContigPosition()
2651 return contig_list; in MapContigPosition()
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| /dports/biology/ncbi-toolkit/ncbi/sequin/ |
| H A D | sequin10.c | 11744 ValNodePtr PNTR contig_list; in GetContigsInScaffoldsCallback() local
11750 || (contig_list = (ValNodePtr PNTR) data) == NULL) { in GetContigsInScaffoldsCallback()
11759 ValNodeAddPointer (contig_list, 0, SeqIdDup (sip)); in GetContigsInScaffoldsCallback()
11898 ValNodePtr contig_list, vnp; in DoRemoveContigsFromScaffolds() local
11907 contig_list = DialogToPointer (frm->list_dlg); in DoRemoveContigsFromScaffolds()
11908 if (contig_list == NULL) { in DoRemoveContigsFromScaffolds()
11915 for (vnp = contig_list; vnp != NULL; vnp = vnp->next) { in DoRemoveContigsFromScaffolds()
11931 ValNodePtr contig_list = NULL; in RemoveContigFromScaffoldMenuItem() local
11948 VisitBioseqsInSep (sep, &contig_list, GetContigsInScaffoldsCallback); in RemoveContigFromScaffoldMenuItem()
11950 if (contig_list == NULL) { in RemoveContigFromScaffoldMenuItem()
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| /dports/biology/plink/plink-ng-79b2df8c/1.9/ |
| H A D | plink_data.c | 9109 Ll_str* contig_list = nullptr; in bcf_to_bed() local
9331 ll_ptr->next = contig_list; in bcf_to_bed()
9333 contig_list = ll_ptr; in bcf_to_bed()
9386 const uint32_t chrom_name_slen = strlen(contig_list->ss); in bcf_to_bed()
9388 …retval = get_or_add_chrom_code(contig_list->ss, ".bcf file", 0, chrom_name_slen, allow_extra_chrom… in bcf_to_bed()
9394 strcpy(&(contigdict[ulii * max_contig_len]), contig_list->ss); in bcf_to_bed()
9396 contig_list = contig_list->next; in bcf_to_bed()
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