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Update batch processing length normalization to match non-batch processing length normalization #441

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merged 4 commits into from
May 16, 2024
Merged

Update batch processing length normalization to match non-batch processing length normalization #441

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0aec950
Update main.cpp
bound-to-love May 14, 2024
d553ea2
Update main.cpp
bound-to-love May 14, 2024
55b0749
Update main.cpp
bound-to-love May 14, 2024
5db77fc
Merge branch 'devel' into master
Yenaled May 16, 2024
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4 changes: 2 additions & 2 deletions src/main.cpp
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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
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See above.

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Could you clarify your question?

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The same problem as in line 2075.

<< "--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(index.target_lens_[i] - ((double)fld_lr[i] / (double)fld_lr_c[i]) - index.k);
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Care to elaborate a bit? Ideally in comment, else maybe at least in the commit message?

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Hi! Based on our analysis for effective length normalization for long reads, the updated effective length provides better results.

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I still don't follow what you are changing and why but I am not familiar with the code. So if this makes sense to others without further explanation, feel free to ignore my comment.

flensout_f << std::fabs(((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