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move numPC check into UD file reading
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@Griffan
Griffan committed Jan 7, 2024
1 parent 9cbc265 commit 8abc12c
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Showing 3 changed files with 124 additions and 128 deletions.
2 changes: 1 addition & 1 deletion CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -65,7 +65,7 @@ target_link_libraries(VerifyBamID statgen Vcf ${HTS_LIBRARIES} samtools ${ZLIB}
enable_testing()
add_test(NAME myTest1
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
COMMAND VerifyBamID --DisableSanityCheck --BamFile resource/test/test.bam --SVDPrefix resource/test/hapmap_3.3.b37.dat --Reference resource/test/chr20.fa.gz)
COMMAND VerifyBamID --DisableSanityCheck --BamFile resource/test/test.bam --SVDPrefix resource/test/hapmap_3.3.b37.dat --Reference resource/test/chr20.fa.gz --NumPC 2)
#add_test( NAME myTest2
# WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
# COMMAND sh ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/run.plot.sh -i ${CMAKE_CURRENT_SOURCE_DIR}/resource/test/hapmap_3.3.b37.dat.V -o ${CMAKE_CURRENT_SOURCE_DIR}/resource/test/hapmap -r 1000g -g grey)
14 changes: 12 additions & 2 deletions ContaminationEstimator.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -264,8 +264,18 @@ int ContaminationEstimator::ReadMatrixUD(const std::string &path) {
}
while (fin.readLine(line)==0) {
std::stringstream ss(line);
for (int index = 0; index != numPC; ++index)
ss >> tmpUD[index];
int index = 0;
while(index < numPC && ss>>tmpUD[index])
{
index++;
}
// Upon finish the line, index == numPC is expected
if (index < numPC) {
warning("--NumPC should be less than or equal to the number of PCs in SVD files provided by --SVDPrefix! (Expected:%d vs Observed:%d)", numPC, index);
warning("--NumPC only permits as large as 4 PCs when using SVD files in ${verifybamID}/resource/ directory!");
warning("You can always prepare you own SVD files with arbitrary number of PCs with --RefVCF enabled.");
exit(EXIT_FAILURE);
}
UD.push_back(tmpUD);
//Initialize arrays
NumMarker++;
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236 changes: 111 additions & 125 deletions main.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -77,137 +77,123 @@ int execute(int argc, char **argv) {
"not specified]")
LONG_STRING_PARAM("Reference", &RefPath, "[String] Reference file[Required]")
LONG_STRING_PARAM("SVDPrefix", &SVDPrefix,
"[String] SVD related files prefix(normally shared by .UD, .mu and .bed files)[Required]")
LONG_STRING_PARAM("Output", &outputPrefix,
"[String] Prefix of output files[optional]")
LONG_PARAM_GROUP("Model Selection Options",
"Options to adjust model selection and parameters")
LONG_PARAM("WithinAncestry", &withinAncestry,
"[Bool] Enabling withinAncestry assume target sample and contamination source are from the same populations,[default:BetweenAncestry] otherwise")
LONG_PARAM("DisableSanityCheck", &disableSanityCheck,
"[Bool] Disable marker quality sanity check(no marker filtering)[default:false]")
LONG_INT_PARAM("NumPC", &nPC,
"[Int] Set number of PCs to infer Allele Frequency[optional]")
LONG_STRING_PARAM("FixPC", &fixPC, "[String] Input fixed PCs to estimate Alpha[format PC1:PC2:PC3...]")
LONG_DOUBLE_PARAM("FixAlpha", &fixAlpha, "[Double] Input fixed Alpha to estimate PC coordinates")
LONG_STRING_PARAM("KnownAF", &knownAF,
"[String] known allele frequency file "
"(chr\tpos\tfreq)[Optional]")
LONG_INT_PARAM("NumThread", &nthread,
"[Int] Set number of threads in likelihood "
"calculation[default:4]")
LONG_INT_PARAM("Seed", &seed,
"[Int] Random number seed[default:12345]")
LONG_DOUBLE_PARAM(
"Epsilon", &epsilon,
"[Double] Minimization procedure convergence "
"threshold, usually a trade-off bettween accuracy and "
"running time[default:1e-10]")
LONG_PARAM("OutputPileup", &outputPileup,
"[Bool] If output temp pileup file")
LONG_PARAM("Verbose", &verbose,
"[Bool] If print the progress of the method on "
"the screen")
LONG_PARAM_GROUP(
"Construction of SVD Auxiliary Files",
"Use these options when generating SVDPrefix files")
LONG_STRING_PARAM(
"RefVCF", &RefVCF,
"[String] VCF file from which to extract reference "
"panel's genotype matrix[Required if no SVD files "
"available]")
LONG_PARAM_GROUP("Pileup Options",
"Arguments for pileup info extraction")
LONG_INT_PARAM(
"min-BQ", &mplp.min_baseQ,
"[Int] skip bases with baseQ/BAQ smaller than min-BQ")
LONG_INT_PARAM(
"min-MQ", &mplp.min_mq,
"[Int] skip alignments with mapQ smaller than min-MQ")
LONG_INT_PARAM("adjust-MQ", &mplp.capQ_thres,
"[Int] adjust mapping quality; "
"recommended:50, disable:0")
LONG_INT_PARAM("max-depth", &mplp.max_depth,
"[Int] max per-file depth")
LONG_PARAM("no-orphans", &noOrphan,
"[Bool] do not use anomalous read pairs")
LONG_INT_PARAM(
"incl-flags", &mplp.flag,
"[Int] required flags: skip reads with mask bits unset")
LONG_INT_PARAM(
"excl-flags", &mplp.rflag_filter,
"[Int] filter flags: skip reads with mask bits set")
"[String] SVD related files prefix(normally shared by .UD, "
".mu and .bed files)[Required]")
LONG_STRING_PARAM("Output", &outputPrefix,
"[String] Prefix of output files[optional]")
LONG_PARAM_GROUP("Model Selection Options",
"Options to adjust model selection and parameters")
LONG_PARAM("WithinAncestry", &withinAncestry,
"[Bool] Enabling withinAncestry assume target sample and "
"contamination source are from the same "
"populations,[default:BetweenAncestry] otherwise")
LONG_PARAM("DisableSanityCheck", &disableSanityCheck,
"[Bool] Disable marker quality sanity check(no marker "
"filtering)[default:false]")
LONG_INT_PARAM("NumPC", &nPC,
"[Int] Set number of PCs to infer Allele Frequency[optional]")
LONG_STRING_PARAM(
"FixPC", &fixPC,
"[String] Input fixed PCs to estimate Alpha[format PC1:PC2:PC3...]")
LONG_DOUBLE_PARAM("FixAlpha", &fixAlpha,
"[Double] Input fixed Alpha to estimate PC coordinates")
LONG_STRING_PARAM("KnownAF", &knownAF,
"[String] known allele frequency file "
"(chr\tpos\tfreq)[Optional]")
LONG_INT_PARAM("NumThread", &nthread,
"[Int] Set number of threads in likelihood "
"calculation[default:4]")
LONG_INT_PARAM("Seed", &seed, "[Int] Random number seed[default:12345]")
LONG_DOUBLE_PARAM("Epsilon", &epsilon,
"[Double] Minimization procedure convergence "
"threshold, usually a trade-off bettween accuracy and "
"running time[default:1e-10]")
LONG_PARAM("OutputPileup", &outputPileup, "[Bool] If output temp pileup file")
LONG_PARAM("Verbose", &verbose,
"[Bool] If print the progress of the method on "
"the screen")
LONG_PARAM_GROUP("Construction of SVD Auxiliary Files",
"Use these options when generating SVDPrefix files")
LONG_STRING_PARAM("RefVCF", &RefVCF,
"[String] VCF file from which to extract reference "
"panel's genotype matrix[Required if no SVD files "
"available]")
LONG_PARAM_GROUP("Pileup Options", "Arguments for pileup info extraction")
LONG_INT_PARAM("min-BQ", &mplp.min_baseQ,
"[Int] skip bases with baseQ/BAQ smaller than min-BQ")
LONG_INT_PARAM("min-MQ", &mplp.min_mq,
"[Int] skip alignments with mapQ smaller than min-MQ")
LONG_INT_PARAM("adjust-MQ", &mplp.capQ_thres,
"[Int] adjust mapping quality; "
"recommended:50, disable:0")
LONG_INT_PARAM("max-depth", &mplp.max_depth, "[Int] max per-file depth")
LONG_PARAM("no-orphans", &noOrphan, "[Bool] do not use anomalous read pairs")
LONG_INT_PARAM("incl-flags", &mplp.flag,
"[Int] required flags: skip reads with mask bits unset")
LONG_INT_PARAM("excl-flags", &mplp.rflag_filter,
"[Int] filter flags: skip reads with mask bits set")

LONG_PARAM_GROUP(
"Deprecated Options",
"These options still are available but not recommended")
LONG_STRING_PARAM("UDPath", &UDPath,
"[String] UD matrix file from SVD result "
"of genotype matrix")
LONG_STRING_PARAM(
"MeanPath", &MeanPath,
"[String] Mean matrix file of genotype matrix")
LONG_STRING_PARAM(
"BedPath", &BedPath,
"[String] Bed file for markers used in this analysis,1 "
"based "
"pos(chr\tpos-1\tpos\trefAllele\taltAllele)[Required]")
END_LONG_PARAMS();
LONG_PARAM_GROUP("Deprecated Options",
"These options still are available but not recommended")
LONG_STRING_PARAM("UDPath", &UDPath,
"[String] UD matrix file from SVD result "
"of genotype matrix")
LONG_STRING_PARAM("MeanPath", &MeanPath,
"[String] Mean matrix file of genotype matrix")
LONG_STRING_PARAM("BedPath", &BedPath,
"[String] Bed file for markers used in this analysis,1 "
"based "
"pos(chr\tpos-1\tpos\trefAllele\taltAllele)[Required]")
END_LONG_PARAMS();

pl.Add(new longParams("Available Options", longParameters));
pl.Read(argc, argv);
pl.Status();
pl.Add(new longParams("Available Options", longParameters));
pl.Read(argc, argv);
pl.Status();

/// Pass along mpileup arguments
if (noOrphan)
mplp.flag |= MPLP_NO_ORPHAN;
else
mplp.flag &= 0XFFFFFFFF ^ MPLP_NO_ORPHAN;
/// End of mpileup parsing
/// Pass along mpileup arguments
if (noOrphan)
mplp.flag |= MPLP_NO_ORPHAN;
else
mplp.flag &= 0XFFFFFFFF ^ MPLP_NO_ORPHAN;
/// End of mpileup parsing

if (nPC > 4) {
error("--NumPC only permits as large as 4 PCs when using "
"SVD files in ${verifybamID}/resource/ directory!");
error("You can always prepare you own SVD files with "
"arbitrary number of PCs with --RefVCF enabled.");
exit(EXIT_FAILURE);
}
if (RefVCF == "Empty") {
if (SVDPrefix == "Empty") {
if (UDPath == "Empty") {
error("--UDPath is required when --RefVCF is absent");
exit(EXIT_FAILURE);
}
if (MeanPath == "Empty") {
error("--MeanPath is required when --RefVCF is absent");
exit(EXIT_FAILURE);
}
if (BedPath == "Empty") {
error("--BedPath is required when --RefVCF is absent");
exit(EXIT_FAILURE);
}
}
else
{
UDPath = SVDPrefix + ".UD";
MeanPath = SVDPrefix + ".mu";
BedPath = SVDPrefix + ".bed";
}
} else//SVD on the fly
{
notice("Specified --RefVCF reference panel VCF file, doing SVD on the fly...");
notice("This procedure will generate SVD matrices as [RefVCF path].UD and [RefVCF path].mu");
notice("You may specify --SVDPrefix [RefVCF path](or --UDPath [RefVCF path].UD and --MeanPath [RefVCF path].mu) in future use");
SVDcalculator calculator;
calculator.ProcessRefVCF(RefVCF);
UDPath = RefVCF+".UD";
MeanPath = RefVCF+".mu";
BedPath = RefVCF+".bed";
notice("Success!");
return 0;
if (RefVCF == "Empty") {
if (SVDPrefix == "Empty") {
if (UDPath == "Empty") {
error("--UDPath is required when --RefVCF is absent");
exit(EXIT_FAILURE);
}
if (MeanPath == "Empty") {
error("--MeanPath is required when --RefVCF is absent");
exit(EXIT_FAILURE);
}
if (BedPath == "Empty") {
error("--BedPath is required when --RefVCF is absent");
exit(EXIT_FAILURE);
}
} else {
UDPath = SVDPrefix + ".UD";
MeanPath = SVDPrefix + ".mu";
BedPath = SVDPrefix + ".bed";
}
} else // SVD on the fly
{
notice(
"Specified --RefVCF reference panel VCF file, doing SVD on the fly...");
notice("This procedure will generate SVD matrices as [RefVCF path].UD and "
"[RefVCF path].mu");
notice("You may specify --SVDPrefix [RefVCF path](or --UDPath [RefVCF "
"path].UD and --MeanPath [RefVCF path].mu) in future use");
SVDcalculator calculator;
calculator.ProcessRefVCF(RefVCF);
UDPath = RefVCF + ".UD";
MeanPath = RefVCF + ".mu";
BedPath = RefVCF + ".bed";
notice("Success!");
return 0;
}

////patch to PC path
////patch to PC path
PCPath=UDPath.substr(0,UDPath.size()-3)+".V";
////

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