Merge branch 'release/4.15.1'

CMakeLists.txt

@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 3.2)
-project(raremetal VERSION 4.15.0 LANGUAGES C CXX Fortran)
+project(raremetal VERSION 4.15.1 LANGUAGES C CXX Fortran)
 
 set(CMAKE_CXX_STANDARD 11)
 

raremetal/src/MetaUtility.cpp

@@ -48,7 +48,7 @@ bool SetIfilePosition(IFILE &sfile, Tabix &myTabix, String Chr, int pos)
 
 // RMW: adjust = 0;
 // RVtest: adjust = 1;
-void tellRvOrRmw(String &buffer, bool &adjust, int marker_col, int cov_col)
+void tellRvOrRmw(String &buffer, bool &adjust, int &marker_col, int &cov_col)
 {
  if (buffer.Find("RareMetalWorker") == -1)
  { // rvt
@@ -60,7 +60,7 @@ void tellRvOrRmw(String &buffer, bool &adjust, int marker_col, int cov_col)
  setFromRvOrRmwAdjust(adjust, marker_col, cov_col);
 }
 
-void setFromRvOrRmwAdjust(bool adjust, int marker_col, int cov_col)
+void setFromRvOrRmwAdjust(bool adjust, int &marker_col, int &cov_col)
 {
  if (adjust)
  { // rv test

raremetal/src/MetaUtility.h

@@ -15,9 +15,9 @@
 /*** file processingpart ***/
 bool SetIfilePosition(IFILE &sfile, Tabix &myTabix, String Chr, int pos);
 
-void tellRvOrRmw(String &buffer, bool &adjust, int marker_col, int cov_col);
+void tellRvOrRmw(String &buffer, bool &adjust, int &marker_col, int &cov_col);
 
-void setFromRvOrRmwAdjust(bool adjust, int marker_col, int cov_col);
+void setFromRvOrRmwAdjust(bool adjust, int &marker_col, int &cov_col);
 
 void openMetaResultFile(String &prefix, String &filename, IFILE &output, String &method);
 

tests/CMakeLists.txt

@@ -91,4 +91,16 @@ run_boilerplate(
  ${BASE_TEST_FOLDER}
  test_tut_rm
  raremetal/test_tut_rm/script.cmake
- ${RM_BIN})
+ ${RM_BIN})
+
+# Test reading of cov files output by rvtests
+set(BASE_TEST_FOLDER ${CMAKE_CURRENT_BINARY_DIR}/test_tut_rm_rvt_cov)
+copy_test_scaffold(
+ ${BASE_TEST_FOLDER}
+ raremetal/test_tut_rm_rvt_cov/inputs/
+ "")
+run_boilerplate(
+ ${BASE_TEST_FOLDER}
+ test_tut_rm_rvt_cov
+ raremetal/test_tut_rm_rvt_cov/script.cmake
+ ${RM_BIN})

tests/raremetal/test_tut_rm_rvt_cov/inputs/group.file

@@ -0,0 +1,6 @@
+GENE1 9:45368740:G:A 9:45375164:C:T 9:45375295:C:T 9:45377254:G:A 9:45377290:C:T 9:45377654:A:G 9:45381530:G:A 9:45381836:C:A 9:45381860:C:T 9:45385488:G:A 9:45389198:G:C
+GENE2 9:45404058:C:T
+GENE3 9:45411110:T:C 9:45412040:C:T 9:45412056:G:A 9:45412079:C:T 9:45412097:G:T
+GENE4 9:45419555:A:G 9:45422446:A:T
+GENE5 9:45445541:C:T 9:45445586:G:A 9:45448036:T:C 9:45448070:G:A 9:45448465:T:G 9:45448507:A:C
+GENE6 9:45451743:C:T 9:45451745:C:G 9:45451769:G:A 9:45451987:G:A 9:45452080:G:A 9:45452429:A:C

tests/raremetal/test_tut_rm_rvt_cov/inputs/rmw.covfiles

@@ -0,0 +1,2 @@
+inputs/STUDY1.QT1.singlevar.cov.txt.gz
+inputs/STUDY2.QT1.singlevar.cov.txt.gz

tests/raremetal/test_tut_rm_rvt_cov/inputs/rmw.summaryfiles

@@ -0,0 +1,2 @@
+inputs/STUDY1.QT1.singlevar.score.txt.gz
+inputs/STUDY2.QT1.singlevar.score.txt.gz

tests/raremetal/test_tut_rm_rvt_cov/inputs/rvtests.covfiles

@@ -0,0 +1,2 @@
+inputs/STUDY1.rvtests.MetaCov.assoc.gz
+inputs/STUDY2.rvtests.MetaCov.assoc.gz

tests/raremetal/test_tut_rm_rvt_cov/inputs/rvtests.summaryfiles

@@ -0,0 +1,2 @@
+inputs/STUDY1.rvtests.MetaScore.assoc.gz
+inputs/STUDY2.rvtests.MetaScore.assoc.gz

tests/raremetal/test_tut_rm_rvt_cov/script.cmake

@@ -0,0 +1,78 @@
+# This script is run as a CMake script; therefore the binary directory may not be the same as for the original build
+# Use CMake variables to pass in context from outside the script
+
+# This script checks for whether raremetal can successfully read and parse
+# summary statistics and cov matrices from both raremetalworker and rvtests for
+# gene-based tests. Inputs include summary statistics and cov matrices output
+# by raremetalworker and rvtests. This test then performs a simple burden test
+# in raremetal with both kinds of input and checks if results are identical
+
+set(BASE_INPUT_DIR ${BASE_TEST_FOLDER}/inputs)
+
+# Delete old outputs before every single run
+set(BASE_OUTPUT_DIR ${BASE_TEST_FOLDER}/output)
+
+if(EXISTS ${BASE_OUTPUT_DIR})
+ file(REMOVE_RECURSE ${BASE_OUTPUT_DIR})
+ message("Existing output directory removed- ${BASE_OUTPUT_DIR}")
+endif()
+
+file(MAKE_DIRECTORY ${BASE_OUTPUT_DIR})
+
+
+# The input files are relative to the root test directory
+# Burden test with input from rvtests
+execute_process(
+ COMMAND ${EXEC_PATH}
+ --summaryFiles ${BASE_INPUT_DIR}/rvtests.summaryfiles
+ --covFiles ${BASE_INPUT_DIR}/rvtests.covfiles
+ --groupFile ${BASE_INPUT_DIR}/group.file
+ --burden
+ --prefix ${BASE_OUTPUT_DIR}/COMBINED.rvtests.QT1 -
+ WORKING_DIRECTORY ${BASE_TEST_FOLDER}
+ RESULT_VARIABLE rm_exit_code
+ OUTPUT_VARIABLE out_text
+ ERROR_VARIABLE out_text)
+
+if(rm_exit_code)
+ message("Result exit code: ${rm_exit_code} - ${EXEC_PATH}")
+ message(FATAL_ERROR "An error was encountered:\n ${out_text}")
+endif()
+
+# Burden test with input from raremetalworker
+execute_process(
+ COMMAND ${EXEC_PATH}
+ --summaryFiles ${BASE_INPUT_DIR}/rmw.summaryfiles
+ --covFiles ${BASE_INPUT_DIR}/rmw.covfiles
+ --groupFile ${BASE_INPUT_DIR}/group.file
+ --burden
+ --prefix ${BASE_OUTPUT_DIR}/COMBINED.rmw.QT1 -
+ WORKING_DIRECTORY ${BASE_TEST_FOLDER}
+ RESULT_VARIABLE rm_exit_code
+ OUTPUT_VARIABLE out_text
+ ERROR_VARIABLE out_text)
+
+if(rm_exit_code)
+ message("Result exit code: ${rm_exit_code} - ${EXEC_PATH}")
+ message(FATAL_ERROR "An error was encountered:\n ${out_text}")
+endif()
+
+# Compare the two sets of meta-analysis results
+set(rvt_b_res COMBINED.rvtests.QT1.meta.burden.results)
+set(rmw_b_res COMBINED.rmw.QT1.meta.burden.results)
+
+if(EXISTS ${BASE_OUTPUT_DIR}/${rvt_b_res} AND EXISTS ${BASE_OUTPUT_DIR}/${rmw_b_res})
+ message("filename is ${BASE_OUTPUT_DIR}/${file}")
+ execute_process(COMMAND diff -q ${BASE_OUTPUT_DIR}/${rvt_b_res} ${BASE_OUTPUT_DIR}/${rmw_b_res} RESULT_VARIABLE diff_exit_code)
+ if(diff_exit_code)
+ message(FATAL_ERROR "Could not replicate expected calculation results for ${BASE_OUTPUT_DIR}/COMBINED.rvtests.QT1.meta.burden.results and ${BASE_OUTPUT_DIR}/COMBINED.rmw.QT1.meta.burden.results.")
+ endif()
+
+else()
+ if(NOT EXISTS ${BASE_OUTPUT_DIR}/${rvt_b_res})
+ message(FATAL_ERROR "The expected output file ${rvt_b_res} was not generated")
+ endif()
+ if(NOT EXISTS ${BASE_OUTPUT_DIR}/${rmw_b_res})
+ message(FATAL_ERROR "The expected output file ${rmw_b_res} was not generated")
+ endif()
+endif()

tests/raremetalworker/test_tut_rmw_kin/expected/STUDY1.QT1.singlevar.cov.txt

@@ -1,5 +1,5 @@
 ##ProgramName=RareMetalWorker
-##Version=4.15.0
+##Version=4.15.1
 #CHROM CURRENT_POS MARKERS_IN_WINDOW COV_MATRICES
 9 400093835 400093835,400306915,400958485,400959725,400978905, 0.362611,-0.0869213,0.00565647,-0.00657949,-0.000774363,
 9 400306915 400306915,400958485,400959725,400978905, 0.30402,0.00026169,0.0267547,-0.00185247,

tests/raremetalworker/test_tut_rmw_kin/expected/STUDY1.QT1.singlevar.score.txt

@@ -1,5 +1,5 @@
 ##ProgramName=RareMetalWorker
-##Version=4.15.0
+##Version=4.15.1
 ##Samples=742
 ##AnalyzedSamples=432
 ##Families=743

tests/raremetalworker/test_tut_rmw_kin/expected/STUDY2.QT1.singlevar.cov.txt

@@ -1,5 +1,5 @@
 ##ProgramName=RareMetalWorker
-##Version=4.15.0
+##Version=4.15.1
 #CHROM CURRENT_POS MARKERS_IN_WINDOW COV_MATRICES
 9 44001280 44001280,44001379,44047825,44047839,44055726,44056400,44056412,44057574,44079591,44081288,44090195,44097343,44098979,44116956,44117052,44117961,44117985,44118188,44118191,44118353,44153100,44153248,44156378,44156472,44159722,44187577,44223113,44223180,44224043,44237864,44302624,44303972,44351815,44352577,44352639,44352665,44352666,44352680,44377205,44377614,44377669,44418077,44418680,44418693,44418824,44470147,44470420,44470679,44470955,44471209,44500701,44501243,44513250,44514741,44514901,44515514,44535999,44536189,44536509,44570393,44570460,44571260,44590874,44610665,44610798,44610843,44611317,44613661,44614208,44635822,44635948,44636131,44636730,44636802,44652954,44660559,44660897,44661139,44661427,44669960,44679167,44680403,44680843,44681185,44681720,44778405,44778489,44778744,44791537,44792701,44793278,44831989,44832875,44832992,44833240,44833851,44890801,44890875,44892168,44932521,44932972,44933419,44933705,44933706,44933895,44933947,44934187,44970935,44979443,44981800,44981832,44981862,44981883,44983567, 0.00829829,0.00764619,-4.36887e-06,-2.7443e-05,-6.31495e-05,1.15126e-06,-0.00114091,-0.00082782,-2.56111e-05,0.00160647,-0.00252938,-1.56423e-05,-0.00023948,-0.00185226,-0.000958411,-2.58346e-05,-0.000109616,0.00574689,-0.001832,0.00574689,-0.00206377,1.13458e-05,-2.57679e-05,-0.00215315,-2.56111e-05,-0.00113654,0.00694232,-3.98927e-05,-6.97152e-06,2.58167e-06,-0.00183076,2.70444e-07,-3.61177e-05,-9.636e-06,-0.000315933,-0.00501038,-0.00282892,-1.60966e-05,-0.000323863,-0.000208891,0.00296668,0.00282546,0.00296637,0.00282546,0.00296668,-0.000224011,0.000235441,-8.57879e-05,-0.000215217,0.00125068,-0.000978069,-1.97915e-05,-0.000132733,-1.10537e-05,-4.6502e-05,-0.00107109,-0.00438066,-0.000146352,-1.3042e-06,-0.00458541,-1.10537e-05,-8.43077e-05,-0.000150853,-0.0048877,-0.0048877,-0.000123141,-1.10537e-05,-0.00327852,-0.00327852,-0.000579695,-6.44851e-06,-1.17712e-05,-1.97361e-05,-0.000987187,0.00139984,-0.000505401,-5.97173e-05,-0.000238196,-7.35079e-05,0.00133518,-2.36199e-05,0.000135915,-1.27148e-05,-6.75556e-05,-1.29919e-05,0.000682725,0.00159444,-1.95388e-05,-4.99702e-05,0.0013259,-4.4672e-05,-0.000632119,0.00208031,0.00208031,-0.000197239,0.000672699,-0.00401123,-9.29902e-05,-3.89141e-05,-0.000139856,-0.00268456,-1.10537e-05,-4.9174e-05,-0.00151299,-2.10025e-05,-0.00279646,-5.01228e-05,0.00200582,0.00276969,-3.89141e-05,-3.89141e-05,-6.02695e-05,0.00276969,0.00273077,
 9 44001379 44001379,44047825,44047839,44055726,44056400,44056412,44057574,44079591,44081288,44090195,44097343,44098979,44116956,44117052,44117961,44117985,44118188,44118191,44118353,44153100,44153248,44156378,44156472,44159722,44187577,44223113,44223180,44224043,44237864,44302624,44303972,44351815,44352577,44352639,44352665,44352666,44352680,44377205,44377614,44377669,44418077,44418680,44418693,44418824,44470147,44470420,44470679,44470955,44471209,44500701,44501243,44513250,44514741,44514901,44515514,44535999,44536189,44536509,44570393,44570460,44571260,44590874,44610665,44610798,44610843,44611317,44613661,44614208,44635822,44635948,44636131,44636730,44636802,44652954,44660559,44660897,44661139,44661427,44669960,44679167,44680403,44680843,44681185,44681720,44778405,44778489,44778744,44791537,44792701,44793278,44831989,44832875,44832992,44833240,44833851,44890801,44890875,44892168,44932521,44932972,44933419,44933705,44933706,44933895,44933947,44934187,44970935,44979443,44981800,44981832,44981862,44981883,44983567,45001346, 0.14882,-0.00080307,-0.000218971,0.0217113,-0.000280532,-0.00996196,-0.00245914,-0.000199586,0.028286,-0.031459,-0.000259647,0.0014279,-0.0343132,-0.0126201,-0.000224212,0.0017631,0.0701643,-0.0337707,0.0701643,-0.0129553,-0.000500296,0.000812544,0.00508485,-0.000199586,-0.00811767,-0.00373234,-0.00102579,-0.000224515,-0.000208539,-0.000473353,-0.000253789,-0.000268602,-0.000210717,-0.00152688,0.00829929,-0.00602516,-0.000284001,-0.00162369,-0.00279627,0.00394164,0.000645539,0.00393666,0.000645539,0.00394164,-0.0033623,0.00362665,0.0034094,-0.00441854,-0.0147015,-0.00344526,-0.000275328,-0.00202258,-0.000256139,0.00102868,-0.00471829,0.0207319,-0.00204153,-0.000131526,-0.00306645,-0.000256139,0.000876405,-0.000594121,0.0063939,0.0063939,0.00738445,-0.000256139,0.0140151,0.0140151,-0.00488309,-0.000289447,-0.000182663,-0.000297506,-0.00208332,0.0187363,-0.000911477,0.000916432,-0.00597591,-0.00192213,-0.0138151,-0.000316193,-0.00110784,0.00118784,-0.00126592,0.00130499,-0.0289992,0.000943766,-0.000328385,0.000637749,-0.0140479,-0.000170679,-0.0146952,-0.0293046,-0.0293046,-0.00136863,-0.0286418,0.030468,0.000369587,-0.000700023,-0.000543298,-0.0332834,-0.000256139,0.00396313,0.0148298,-0.000238585,-0.0327702,-0.00215091,0.012213,0.00958876,-0.000700023,-0.000700023,-5.78115e-07,0.00958876,0.00888877,0.0117845,

tests/raremetalworker/test_tut_rmw_kin/expected/STUDY2.QT1.singlevar.score.txt

@@ -1,5 +1,5 @@
 ##ProgramName=RareMetalWorker
-##Version=4.15.0
+##Version=4.15.1
 ##Samples=8848
 ##AnalyzedSamples=591
 ##Families=598

tests/raremetalworker/test_tut_rmw_nokin/expected/STUDY1.QT1.singlevar.cov.txt

@@ -1,5 +1,5 @@
 ##ProgramName=RareMetalWorker
-##Version=4.15.0
+##Version=4.15.1
 #CHROM CURRENT_POS MARKERS_IN_WINDOW COV_MATRICES
 9 400093835 400093835,400306915,400958485,400959725,400978905, 0.441133,-0.107416,0.00696527,-0.00773918,-0.000773918,
 9 400306915 400306915,400958485,400959725,400978905, 0.35842,0.000712725,0.0318458,-0.00208418,

tests/raremetalworker/test_tut_rmw_nokin/expected/STUDY1.QT1.singlevar.score.txt

@@ -1,5 +1,5 @@
 ##ProgramName=RareMetalWorker
-##Version=4.15.0
+##Version=4.15.1
 ##Samples=742
 ##AnalyzedSamples=432
 ##Families=743

tests/raremetalworker/test_tut_rmw_nokin/expected/STUDY2.QT1.singlevar.cov.txt

@@ -1,5 +1,5 @@
 ##ProgramName=RareMetalWorker
-##Version=4.15.0
+##Version=4.15.1
 #CHROM CURRENT_POS MARKERS_IN_WINDOW COV_MATRICES
 9 44001280 44001280,44001379,44047825,44047839,44055726,44056400,44056412,44057574,44079591,44081288,44090195,44097343,44098979,44116956,44117052,44117961,44117985,44118188,44118191,44118353,44153100,44153248,44156378,44156472,44159722,44187577,44223113,44223180,44224043,44237864,44302624,44303972,44351815,44352577,44352639,44352665,44352666,44352680,44377205,44377614,44377669,44418077,44418680,44418693,44418824,44470147,44470420,44470679,44470955,44471209,44500701,44501243,44513250,44514741,44514901,44515514,44535999,44536189,44536509,44570393,44570460,44571260,44590874,44610665,44610798,44610843,44611317,44613661,44614208,44635822,44635948,44636131,44636730,44636802,44652954,44660559,44660897,44661139,44661427,44669960,44679167,44680403,44680843,44681185,44681720,44778405,44778489,44778744,44791537,44792701,44793278,44831989,44832875,44832992,44833240,44833851,44890801,44890875,44892168,44932521,44932972,44933419,44933705,44933706,44933895,44933947,44934187,44970935,44979443,44981800,44981832,44981862,44981883,44983567, 0.00840709,0.00862515,-2.86931e-05,-1.43466e-05,-0.000137727,-1.43466e-05,-0.0012338,-0.000731675,-1.43466e-05,0.00253647,-0.00303286,-1.43466e-05,-0.000286931,-0.00299556,-0.00121946,-1.43466e-05,-5.73863e-05,0.00744874,-0.00296831,0.00744874,-0.00281193,-2.86931e-05,-2.86931e-05,-0.0018794,-1.43466e-05,-0.00127684,0.00767541,-5.74835e-05,-1.43466e-05,-1.43466e-05,-0.00353499,-1.43466e-05,-1.43709e-05,-1.43466e-05,2.30324e-05,-0.00673141,-0.00465396,-1.43466e-05,-0.000200852,-0.000286931,0.00500121,0.00481471,0.00500092,0.00481471,0.00500121,-0.000315624,0.00033053,-5.73863e-05,-0.000401704,0.00120715,-0.000890995,-1.43466e-05,-0.000129119,-1.43466e-05,-2.86931e-05,-0.00104443,-0.0066195,-0.000286931,-1.43466e-05,-0.00636414,-1.43466e-05,-2.86931e-05,-0.000100426,-0.00721919,-0.00721919,-0.000456221,-1.43466e-05,-0.00588496,-0.00588496,-0.000401704,-1.43466e-05,-1.43466e-05,-1.43466e-05,-0.000890995,7.18545e-05,-0.000659942,-2.86931e-05,-0.000602556,-8.60794e-05,0.00274593,-1.43466e-05,0.000104492,-1.43466e-05,-7.17328e-05,-1.43466e-05,0.00165846,0.00162403,-1.43466e-05,-5.73863e-05,0.00273159,-1.43466e-05,-0.00105878,0.00319355,0.00319355,-8.60794e-05,0.00167281,-0.00580988,-0.000129119,-2.86931e-05,-0.000100426,-0.00411007,-1.43466e-05,-2.90869e-05,-0.00177897,-1.43466e-05,-0.00434414,-0.000100426,0.00309786,0.004413,-2.86931e-05,-2.86931e-05,-8.60794e-05,0.004413,0.00438431,
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tests/raremetalworker/test_tut_rmw_nokin/expected/STUDY2.QT1.singlevar.score.txt

@@ -1,5 +1,5 @@
 ##ProgramName=RareMetalWorker
-##Version=4.15.0
+##Version=4.15.1
 ##Samples=8848
 ##AnalyzedSamples=591
 ##Families=598