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Add option to produce only singlets probabilities (fix #52) #55

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Add option to produce only singlets probabilities (fix #52) #55

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6 changes: 6 additions & 0 deletions cmd_cram_demuxlet.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@ int32_t main(int32_t argc, char** argv) {
vr.vfilt.minCallRate = 0.5;
vr.vfilt.maxAlleles = 2;
bool writePair = false;
bool onlySinglets = false;
//bool fullPair = true;
double doublet_prior = 0.5;
std::string groupList;
Expand Down Expand Up @@ -53,6 +54,7 @@ int32_t main(int32_t argc, char** argv) {
LONG_STRING_PARAM("out",&outPrefix,"Output file prefix")
LONG_MULTI_DOUBLE_PARAM("alpha",&gridAlpha, "Grid of alpha to search for (default is 0, 0.5)")
LONG_PARAM("write-pair",&writePair, "Writing the (HUGE) pair file")
LONG_PARAM("only-singlets", &onlySinglets, "If set, only singlets probabilities are computed and saved to file with extension .single. Will not compute doublet and best assignments.")
LONG_DOUBLE_PARAM("doublet-prior",&doublet_prior, "Prior of doublet")
LONG_INT_PARAM("sam-verbose",&sr.verbose, "Verbose message frequency for SAM/BAM/CRAM")
LONG_INT_PARAM("vcf-verbose",&vr.verbose, "Verbose message frequency for VCF/BCF")
Expand Down Expand Up @@ -525,6 +527,10 @@ int32_t main(int32_t argc, char** argv) {
}
notice("Finished processing %d droplets total", i);
hts_close(wsingle);
if(onlySinglets) {
notice("Finished processing singlets, will not process doublets.");
return 0;
}

htsFile* wsing2 = hts_open((outPrefix+".sing2").c_str(),"w");
htsFile* wpair = (writePair ? hts_open((outPrefix+".pair").c_str(),"w") : NULL);
Expand Down