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Removing outliers from raw signal #521

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Removing outliers from raw signal #521

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9e732d0
Update nanopolish_fast5_io.cpp
awjga Dec 20, 2018
5542f1a
Remove outliers from raw signal
awjga Dec 20, 2018
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16 changes: 15 additions & 1 deletion src/common/nanopolish_fast5_io.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -92,7 +92,8 @@ raw_table fast5_get_raw_samples(hid_t hdf5_file, fast5_raw_scaling scaling)
herr_t status;
float raw_unit;
raw_table rawtbl = { 0, 0, 0, NULL };

size_t tmp_nsample;

// mostly from scrappie
std::string raw_read_group = fast5_get_raw_read_group(hdf5_file);

Expand Down Expand Up @@ -132,6 +133,19 @@ raw_table fast5_get_raw_samples(hid_t hdf5_file, fast5_raw_scaling scaling)
rawptr[i] = (rawptr[i] + scaling.offset) * raw_unit;
}

// filter the outliers in pA
for (size_t i = nsample-1; i >0 ; i--) {
//filter sample > 200 pA and less than 0 pA
if(rawptr[i]>200 || rawptr[i]<0){
tmp_nsample=tmp_nsample-1;
for (size_t dd=i;dd<nsample;dd++){
rawptr[dd]=rawptr[dd+1];
}
}
}
//to update the value of rawtbl
nsample=tmp_nsample;
rawtbl = (raw_table) { nsample, 0, nsample, rawptr };
cleanup4:
H5Sclose(space);
cleanup3:
Expand Down