From 9e732d0936336b150c98f328971e17d4b1a397d8 Mon Sep 17 00:00:00 2001
From: awjga <30524842+awjga@users.noreply.github.com>
Date: Thu, 20 Dec 2018 11:32:49 +0800
Subject: [PATCH 1/2] Update nanopolish_fast5_io.cpp

To remove outliers in raw signal
---
 src/common/nanopolish_fast5_io.cpp | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/src/common/nanopolish_fast5_io.cpp b/src/common/nanopolish_fast5_io.cpp
index 7f387192..a13e3750 100644
--- a/src/common/nanopolish_fast5_io.cpp
+++ b/src/common/nanopolish_fast5_io.cpp
@@ -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);
 
@@ -132,6 +133,20 @@ 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
+    // this is edited by awjga
+    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:

From 5542f1a07a2cc7aad158b57dd7432dbd1ac9eb05 Mon Sep 17 00:00:00 2001
From: awjga <30524842+awjga@users.noreply.github.com>
Date: Thu, 20 Dec 2018 11:42:01 +0800
Subject: [PATCH 2/2] Remove outliers from raw signal

---
 src/common/nanopolish_fast5_io.cpp | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/common/nanopolish_fast5_io.cpp b/src/common/nanopolish_fast5_io.cpp
index a13e3750..7416bc60 100644
--- a/src/common/nanopolish_fast5_io.cpp
+++ b/src/common/nanopolish_fast5_io.cpp
@@ -134,7 +134,6 @@ raw_table fast5_get_raw_samples(hid_t hdf5_file, fast5_raw_scaling scaling)
     }
 
     // filter the outliers in pA
-    // this is edited by awjga
     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){