From 1b524e32d8f4bc313ce5f88d587f3b61f4e4f80f Mon Sep 17 00:00:00 2001
From: Valentina Boeva <valeu@users.noreply.github.com>
Date: Thu, 16 Mar 2017 15:13:09 +0100
Subject: [PATCH 1/2] Delete RSSerror.h

---
 src/RSSerror.h | 25 -------------------------
 1 file changed, 25 deletions(-)
 delete mode 100644 src/RSSerror.h

diff --git a/src/RSSerror.h b/src/RSSerror.h
deleted file mode 100644
index 70b450d..0000000
--- a/src/RSSerror.h
+++ /dev/null
@@ -1,25 +0,0 @@
-#pragma once
-#ifndef RSSERROR_H
-#define RSSERROR_H
-
-#include <iostream>
-#include <stdlib.h>
-#include <fstream>
-#include <vector>
-#include <string>
-#include <math.h>
-#include <algorithm>
-#include <map>
-#include "GenomeCopyNumber.h"
-#include "ChrCopyNumber.h"
-
-
-class RSSerror
-{
-    public:
-        RSSerror();
-};
-
-long double calculateRSS(GenomeCopyNumber & samplecopynumber, int ploidy);
-
-#endif // RSSERROR_H

From b75642afb3b13e45589ec70671af03bb8109ae7f Mon Sep 17 00:00:00 2001
From: Valentina Boeva <valeu@users.noreply.github.com>
Date: Thu, 16 Mar 2017 15:13:22 +0100
Subject: [PATCH 2/2] Delete RSSerror.cpp

---
 src/RSSerror.cpp | 52 ------------------------------------------------
 1 file changed, 52 deletions(-)
 delete mode 100644 src/RSSerror.cpp

diff --git a/src/RSSerror.cpp b/src/RSSerror.cpp
deleted file mode 100644
index e675976..0000000
--- a/src/RSSerror.cpp
+++ /dev/null
@@ -1,52 +0,0 @@
-#include "RSSerror.h"
-
-using namespace std;
-
-RSSerror::RSSerror()
-{
-}
-
-long double calculateRSS(GenomeCopyNumber & samplecopynumber, int ploidy)
-{
-    string::size_type pos = 0;
-    vector<float> observedvalues;
-    vector<float> expectedvalues;
-	map<string,int>::iterator it;
-	for ( it=samplecopynumber.chromosomesInd_.begin() ; it != samplecopynumber.chromosomesInd_.end(); it++ ) {
-		string chrNumber = (*it).first;
-		if ( ( pos = chrNumber.find("chr", pos)) != string::npos )
-			chrNumber.replace( pos, 3, "" );
-        if ( ( pos = chrNumber.find("X", pos)) != string::npos ) 		//exclude X and Y from the analysis
-            continue;
-        if ( ( pos = chrNumber.find("Y", pos)) != string::npos )
-            continue;
-		int index = samplecopynumber.findIndex(chrNumber);
-		int length = samplecopynumber.chrCopyNumber_[index].getLength();
-		for (int i = 0; i< length; i++) {
-            float observed = 0;
-            float expected = 0;
-                {
-                observed = samplecopynumber.chrCopyNumber_[index].getRatioAtBin(i);
-                expected = observed;
-                if (samplecopynumber.chrCopyNumber_[index].isMedianCalculated()) {
-                    expected = samplecopynumber.chrCopyNumber_[index].getMedianProfileAtI(i);
-                    if (samplecopynumber.chrCopyNumber_[index].isSmoothed())
-                        expected = samplecopynumber.chrCopyNumber_[index].getSmoothedProfileAtI(i);
-                    }
-                }
-			observedvalues.push_back(observed);
-			expectedvalues.push_back(expected);
-		}
-	}
-
-    long double RSS = 0;
-    for (int i = 0; i < (int)observedvalues.size(); i++)
-        {
-        if ((observedvalues[i]!=NA) && (expectedvalues[i]!=NA))
-            {
-            long double diff = (long double)observedvalues[i] - (long double)round(ploidy*expectedvalues[i])/ploidy;
-            RSS = RSS + (long double)pow(diff,2);
-            }
-        }
-    return RSS;
-}