Skip to content

Revert "Update batch processing length normalization to match non-batch processing length normalization" #442

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
Yenaled wants to merge 1 commit into
base: devel
Choose a base branch
from
Open

Revert "Update batch processing length normalization to match non-batch processing length normalization" #442

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions src/main.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2190,7 +2190,7 @@ void usageTCCQuant(bool valid_input = true) {
<< " (default: equivalence classes are taken from the index)" << endl
<< "-f, --fragment-file=FILE File containing fragment length distribution" << endl
<< " (default: effective length normalization is not performed)" << endl
<< "--long Use version of EM for long reads " << endl
<< "--long Use version of EM for long reads " << endl
<< "-P, --platform. [PacBio or ONT] used for sequencing " << endl
<< "-l, --fragment-length=DOUBLE Estimated average fragment length" << endl
<< "-s, --sd=DOUBLE Estimated standard deviation of fragment length" << endl
Expand Down Expand Up @@ -2390,7 +2390,7 @@ int main(int argc, char *argv[]) {
if (fld_lr_c[i] > 0.5) {
//Good results with comment below.
//flensout_f << std::fabs((double)fld_lr[i] / (double)fld_lr_c[i] - index.k);//index.target_lens_[i] - (double)fld_lr[i] / (double)fld_lr_c[i] - k); // take mean of recorded uniquely aligning read lengths
flensout_f << std::fabs(((double)fld_lr[i] / (double)fld_lr_c[i]) - index.k);
flensout_f << std::fabs(index.target_lens_[i] - ((double)fld_lr[i] / (double)fld_lr_c[i]) - index.k);
} else {
flensout_f << std::fabs(index.target_lens_[i] - index.k);//index.target_lens_[i]);
}
Expand Down