[med-svn] [qtltools] 03/03: Merge tag 'upstream/1.0+dfsg'
Dylan Aïssi
bob.dybian-guest at moszumanska.debian.org
Thu Nov 24 21:00:27 UTC 2016
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bob.dybian-guest pushed a commit to branch master
in repository qtltools.
commit 6d98950c256bbd6a804a7e1a7672bde69117bbc0
Merge: 0e234b8 288141d
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date: Thu Nov 24 21:59:46 2016 +0100
Merge tag 'upstream/1.0+dfsg'
Upstream version 1.0+dfsg
LICENSE | 621 +++++++++++++++++++++
Makefile | 245 ++++++++
README | 8 +
lib/OTools/basic_stats.h | 87 +++
lib/OTools/compressed_io.h | 93 +++
lib/OTools/full_linear_regression.h | 102 ++++
lib/OTools/genomic_region.h | 103 ++++
lib/OTools/interval_tree.h | 274 +++++++++
lib/OTools/otools.h | 80 +++
lib/OTools/pca.h | 230 ++++++++
lib/OTools/random_number.h | 68 +++
lib/OTools/ranker.h | 238 ++++++++
lib/OTools/residualizer.h | 195 +++++++
lib/OTools/string_utils.h | 72 +++
lib/OTools/timer.h | 69 +++
lib/OTools/verbose.h | 121 ++++
script/plotTrans.R | 59 ++
script/runFDR_atrans.R | 25 +
script/runFDR_cis.R | 67 +++
script/runFDR_ftrans.R | 25 +
src/QTLtools.cpp | 133 +++++
src/common/data.cpp | 287 ++++++++++
src/common/data.h | 73 +++
src/common/filter.h | 87 +++
src/mode_ase/ase_data.h | 102 ++++
src/mode_ase/ase_main.cpp | 102 ++++
src/mode_ase/ase_read_genotypes.cpp | 118 ++++
src/mode_ase/ase_read_sequences.cpp | 180 ++++++
src/mode_bamstat/bamstat_data.h | 80 +++
src/mode_bamstat/bamstat_main.cpp | 80 +++
src/mode_bamstat/bamstat_read_annotations.cpp | 36 ++
src/mode_bamstat/bamstat_read_bam.cpp | 161 ++++++
src/mode_bamstat/bamstat_write_output.cpp | 23 +
src/mode_cis/cis_chunking.cpp | 190 +++++++
src/mode_cis/cis_collapse_phenotypes.cpp | 82 +++
src/mode_cis/cis_conditionnal_pass.cpp | 207 +++++++
src/mode_cis/cis_data.h | 184 ++++++
src/mode_cis/cis_initilization.cpp | 66 +++
src/mode_cis/cis_learn_beta.cpp | 103 ++++
src/mode_cis/cis_learn_dof.cpp | 99 ++++
src/mode_cis/cis_main.cpp | 201 +++++++
src/mode_cis/cis_management.cpp | 94 ++++
src/mode_cis/cis_nominal_pass.cpp | 135 +++++
src/mode_cis/cis_permutation_pass.cpp | 195 +++++++
src/mode_cis/cis_read_covariates.cpp | 56 ++
src/mode_cis/cis_read_genotypes.cpp | 215 +++++++
src/mode_cis/cis_read_phenotypes.cpp | 157 ++++++
src/mode_cis/cis_read_thresholds.cpp | 57 ++
src/mode_correct/correct_data.h | 66 +++
src/mode_correct/correct_main.cpp | 100 ++++
src/mode_correct/correct_management.cpp | 91 +++
src/mode_correct/correct_processing.cpp | 114 ++++
src/mode_correct/correct_read_covariates.cpp | 52 ++
src/mode_extract/extract_data.h | 56 ++
src/mode_extract/extract_main.cpp | 88 +++
src/mode_extract/extract_managment.cpp | 39 ++
src/mode_extract/extract_read_data.cpp | 198 +++++++
src/mode_extract/extract_write.cpp | 45 ++
src/mode_fdensity/fdensity_data.h | 63 +++
src/mode_fdensity/fdensity_main.cpp | 86 +++
src/mode_fdensity/fdensity_process.cpp | 84 +++
src/mode_fdensity/fdensity_read_annotation.cpp | 44 ++
src/mode_fdensity/fdensity_read_qtl.cpp | 42 ++
src/mode_fenrich/fenrich_data.h | 73 +++
src/mode_fenrich/fenrich_main.cpp | 86 +++
src/mode_fenrich/fenrich_management.cpp | 80 +++
src/mode_fenrich/fenrich_process.cpp | 64 +++
src/mode_fenrich/fenrich_read_annotation.cpp | 44 ++
src/mode_fenrich/fenrich_read_qtl.cpp | 38 ++
src/mode_fenrich/fenrich_read_tss.cpp | 42 ++
src/mode_genrich/genrich_binning_process.cpp | 61 ++
src/mode_genrich/genrich_data.h | 83 +++
src/mode_genrich/genrich_main.cpp | 106 ++++
src/mode_genrich/genrich_process.cpp | 110 ++++
src/mode_genrich/genrich_read_auxillliary_data.cpp | 66 +++
src/mode_genrich/genrich_read_phenotypes.cpp | 76 +++
.../genrich_read_reference_genotypes.cpp | 101 ++++
src/mode_genrich/genrich_routines.cpp | 52 ++
src/mode_match/match_data.h | 106 ++++
src/mode_match/match_main.cpp | 98 ++++
src/mode_match/match_managment.cpp | 32 ++
src/mode_match/match_process.cpp | 67 +++
src/mode_match/match_read_genotypes.cpp | 121 ++++
src/mode_match/match_read_sequences.cpp | 103 ++++
src/mode_pca/pca_data.h | 58 ++
src/mode_pca/pca_main.cpp | 102 ++++
src/mode_pca/pca_management.cpp | 64 +++
src/mode_pca/pca_pca.cpp | 240 ++++++++
src/mode_pca/pca_pca.h | 161 ++++++
src/mode_pca/pca_read_data.cpp | 287 ++++++++++
src/mode_quan/quan_chunking.cpp | 42 ++
src/mode_quan/quan_data.h | 277 +++++++++
src/mode_quan/quan_main.cpp | 166 ++++++
src/mode_quan/quan_management.cpp | 41 ++
src/mode_quan/quan_printResults.cpp | 136 +++++
src/mode_quan/quan_readBAM.cpp | 398 +++++++++++++
src/mode_quan/quan_readGTF.cpp | 102 ++++
src/mode_rtc/rtc_chunking.cpp | 167 ++++++
src/mode_rtc/rtc_collapse_phenotypes.cpp | 83 +++
src/mode_rtc/rtc_common.cpp | 492 ++++++++++++++++
src/mode_rtc/rtc_data.h | 506 +++++++++++++++++
src/mode_rtc/rtc_gwas_cis.cpp | 137 +++++
src/mode_rtc/rtc_gwas_trans.cpp | 135 +++++
src/mode_rtc/rtc_initilization.cpp | 80 +++
src/mode_rtc/rtc_main.cpp | 384 +++++++++++++
src/mode_rtc/rtc_management.cpp | 196 +++++++
src/mode_rtc/rtc_mergeQTL_cis.cpp | 148 +++++
src/mode_rtc/rtc_mergeQTL_trans.cpp | 148 +++++
src/mode_rtc/rtc_read_covariates.cpp | 55 ++
src/mode_rtc/rtc_read_genotypes.cpp | 430 ++++++++++++++
src/mode_rtc/rtc_read_get_hotspots.cpp | 113 ++++
src/mode_rtc/rtc_read_phenotypes.cpp | 181 ++++++
src/mode_rtc/rtc_sampling.cpp | 312 +++++++++++
src/mode_trans/trans_adjust.cpp | 52 ++
src/mode_trans/trans_analysis_pass.cpp | 117 ++++
src/mode_trans/trans_chunking.cpp | 31 +
src/mode_trans/trans_data.h | 148 +++++
src/mode_trans/trans_initilization.cpp | 52 ++
src/mode_trans/trans_learn_beta.cpp | 103 ++++
src/mode_trans/trans_main.cpp | 161 ++++++
src/mode_trans/trans_managment.cpp | 161 ++++++
src/mode_trans/trans_read_covariates.cpp | 67 +++
src/mode_trans/trans_read_phenotypes.cpp | 116 ++++
src/mode_trans/trans_read_samples.cpp | 93 +++
src/mode_union/union_data.h | 247 ++++++++
src/mode_union/union_initilization.cpp | 91 +++
src/mode_union/union_main.cpp | 153 +++++
src/mode_union/union_management.cpp | 257 +++++++++
src/mode_union/union_read_covariates.cpp | 57 ++
src/mode_union/union_read_genotypes.cpp | 374 +++++++++++++
src/mode_union/union_read_get_hotspots.cpp | 88 +++
src/mode_union/union_read_phenotypes.cpp | 153 +++++
src/mode_union/union_union.cpp | 170 ++++++
133 files changed, 17394 insertions(+)
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