Package: QUILT 2.0.4.9000

Sounkou Mahamane Toure

QUILT: QUILT

QUILT2 is an R and C++ program for fast genotype calling from sequencing reads using a large reference panel. QUILT2 is accurate and versatile, able to handle imputation from short read, long read, ancient DNA and cell-free DNA from NIPT.

Authors:Sounkou Mahamane Toure [aut, cre], Abiomix FZ LLC [cph, fnd], Robert Davies [aut], Zilong Li [aut]

QUILT_2.0.4.9000.tar.gz

QUILT_2.0.4.9000.tgz(r-4.6-x86_64)QUILT_2.0.4.9000.tgz(r-4.6-arm64)
QUILT_2.0.4.9000.tar.gz(r-4.7-arm64)QUILT_2.0.4.9000.tar.gz(r-4.7-x86_64)QUILT_2.0.4.9000.tar.gz(r-4.6-arm64)QUILT_2.0.4.9000.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
QUILT/json (API)

# Install 'QUILT' in R:
install.packages('QUILT', repos = c('https://abiomix.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/abiomix/abiomix-r-open/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

openblascpp

2.19 score 31 scripts 81 exports 6 dependencies

Last updated from:dd82290ba2. Checks:6 ERROR, 1 OK, 6 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64ERROR377
linux-devel-x86_64ERROR356
source / vignettesOK362
linux-release-arm64ERROR351
linux-release-x86_64ERROR368
macos-release-arm64ERROR279
macos-release-x86_64ERROR544
macos-oldrel-arm64FAIL132
macos-oldrel-x86_64FAIL301
windows-develFAIL149
windows-releaseFAIL108
windows-oldrelFAIL123
wasm-releaseFAIL96

Exports:calculate_likelihoods_valuesincrement2Nmake_quilt_fb_test_packagemake_reference_single_test_packagemodified_calculate_pseQUILTquilt_chunk_mapQUILT_HLAQUILT_HLA_prepare_referenceQUILT_prepare_referencer2_by_freqrcpp_alpha_forward_onercpp_alpha_forward_one_QUILT_fasterrcpp_apply_mat_relabelrcpp_apply_vec_relabelRcpp_block_gibbs_resamplerRcpp_build_eMatDHrcpp_calc_prob_of_set_of_readsrcpp_calculate_block_read_label_probabilities_using_H_classrcpp_calculate_genProbs_and_hapProbs_final_rare_commonrcpp_calculate_gibbs_small_genProbs_and_hapProbs_using_binary_objectsrcpp_calculate_gn_genProbs_and_hapProbsrcpp_consider_and_try_entire_relabellingRcpp_consider_block_relabellingRcpp_consider_total_relabellingRcpp_define_blocked_snps_using_gamma_on_the_flyrcpp_determine_label_probabilitiesrcpp_determine_where_to_stoprcpp_evaluate_read_probabilitiesrcpp_evaluate_read_variabilityRcpp_fill_rlcMrcpp_fly_weighterrcpp_forwardBackwardGibbsNIPTrcpp_get_log_p_H_classrcpp_get_log_p_H_class2Rcpp_get_top_K_or_more_matches_while_building_gammaRcpp_get_top_K_or_more_matches_while_building_gamma_eigenrcpp_get_weights_for_entire_relabellingRcpp_gibbs_block_forward_onercpp_gibbs_nipt_initializercpp_gibbs_nipt_iterateRcpp_haploid_dosage_versus_refsRcpp_haploid_reference_single_backwardRcpp_haploid_reference_single_backward_version2Rcpp_haploid_reference_single_backward_version3Rcpp_haploid_reference_single_forwardRcpp_haploid_reference_single_forward_version2Rcpp_haploid_reference_single_forward_version3rcpp_initialize_gibbs_forward_backwardrcpp_internal_make_eMatRead_t_using_binaryrcpp_make_eMatGrid_trcpp_make_eMatRead_tRcpp_make_eMatRead_t_for_final_rare_common_gibbs_using_objectsRcpp_make_eMatRead_t_for_gibbs_using_objectsrcpp_make_fb_snp_offsetsRcpp_make_gibbs_considersRcpp_make_gl_boundrcpp_make_rescaled_on_fly_eMatGrid_trcpp_make_smoothed_ratercpp_nth_partial_sortRcpp_quilt_test_doublerRcpp_raw_testRcpp_raw_test_intrcpp_reinitialize_in_iterationsRcpp_reset_local_variablesRcpp_run_backward_haploidRcpp_run_backward_haploid_QUILT_fasterRcpp_run_forward_haploidrcpp_sample_H_using_H_classRcpp_shard_block_gibbs_resamplerrcpp_simple_binary_matrix_searchrcpp_simple_binary_searchrcpp_simple_quantileRcpp_testrcpp_test_one_based_swaprcpp_test1rcpp_test2rcpp_test3rcpp_test4rcpp_test5sample_reads_in_grid

Dependencies:data.tablemspbwtRcppRcppArmadilloRcppEigenSTITCH

Readme and manuals

Help Manual

Help pageTopics
QUILTQUILT
QUILT_HLAQUILT_HLA
QUILT_HLA_prepare_referenceQUILT_HLA_prepare_reference
QUILT_prepare_referenceQUILT_prepare_reference