Index

A

analyze_bam() (xyalign.bam.BamFile method)

B

bam_analysis() (in module xyalign.xyalign) BamFile (class in xyalign.bam)

before_after_plot() (in module xyalign.utils) bootstrap() (in module xyalign.ploidy) bwa_mem_mapping_sambamba() (in module xyalign.assemble)

C

check_bam_fasta_compatibility() (in module xyalign.utils) check_bwa_index() (xyalign.reftools.RefFasta method) check_chrom_in_bam() (xyalign.bam.BamFile method) check_compatibility_bam_list() (in module xyalign.utils) check_seq_dict() (xyalign.reftools.RefFasta method) chrom_counts() (xyalign.bam.BamFile method) chrom_stats() (in module xyalign.xyalign) (xyalign.bam.BamFile method) chromosome_bed() (xyalign.bam.BamFile method) (xyalign.reftools.RefFasta method)

chromosome_lengths() (xyalign.bam.BamFile method) (xyalign.reftools.RefFasta method) chromosome_names() (xyalign.bam.BamFile method) (xyalign.reftools.RefFasta method) chromosome_wide_plot() (in module xyalign.utils) compress_vcf() (xyalign.variants.VCFFile method) conditional_index_bwa() (xyalign.reftools.RefFasta method) conditional_seq_dict() (xyalign.reftools.RefFasta method)

E

extract_read_group() (xyalign.bam.BamFile method)

extract_regions() (xyalign.bam.BamFile method)

G

get_chrom_length() (xyalign.bam.BamFile method) (xyalign.reftools.RefFasta method)

H

hist_array() (in module xyalign.utils)

hist_read_balance() (in module xyalign.variants)

I

index_bam() (xyalign.bam.BamFile method) index_bwa() (xyalign.reftools.RefFasta method) index_fai() (xyalign.reftools.RefFasta method) index_vcf() (xyalign.variants.VCFFile method)

is_bgzipped() (xyalign.variants.VCFFile method) is_faidxed() (xyalign.reftools.RefFasta method) is_indexed() (xyalign.bam.BamFile method) isolate_chroms() (xyalign.reftools.RefFasta method)

K

ks_two_sample() (in module xyalign.ploidy)

M

main() (in module xyalign.xyalign) make_region_lists_chromosome_filters() (in module xyalign.utils)

make_region_lists_genome_filters() (in module xyalign.utils) mask_reference() (xyalign.reftools.RefFasta method) merge_bed_files() (in module xyalign.utils)

O

output_bed() (in module xyalign.utils)

output_bed_no_merge() (in module xyalign.utils)

P

parse_args() (in module xyalign.xyalign) parse_platypus_VCF() (xyalign.variants.VCFFile method) permutation_test_chromosomes() (in module xyalign.ploidy) platypus_caller() (xyalign.bam.BamFile method)

ploidy_analysis() (in module xyalign.xyalign) plot_depth_mapq() (in module xyalign.utils) plot_read_balance() (in module xyalign.variants) plot_variants_per_chrom() (xyalign.variants.VCFFile method)

R

read_balance_per_window() (in module xyalign.variants) ref_prep() (in module xyalign.xyalign)

RefFasta (class in xyalign.reftools) remapping() (in module xyalign.xyalign)

S

samtools_merge() (in module xyalign.bam) seq_dict() (xyalign.reftools.RefFasta method) sort_bam() (xyalign.bam.BamFile method)

strip_reads() (xyalign.bam.BamFile method) swap_sex_chroms() (in module xyalign.xyalign) switch_sex_chromosomes_sambamba() (in module xyalign.bam)

V

validate_dir() (in module xyalign.utils)

validate_external_prog() (in module xyalign.utils) VCFFile (class in xyalign.variants)

X

xyalign (module) xyalign.assemble (module) xyalign.bam (module) xyalign.ploidy (module)

xyalign.reftools (module) xyalign.utils (module) xyalign.variants (module) xyalign.xyalign (module)