Index: test/tools/llvm-objcopy/adjacent-segments.test
===================================================================
--- /dev/null
+++ test/tools/llvm-objcopy/adjacent-segments.test
@@ -0,0 +1,62 @@
+# This test tests that if two non-overlapping segments are right next to each
+# other no problems arise.
+
+# RUN: yaml2obj %s -o %t
+# RUN: llvm-objcopy %t %t2
+# RUN: llvm-readobj --program-headers %t2 | FileCheck %s
+
+!ELF
+FileHeader:
+  Class:           ELFCLASS64
+  Data:            ELFDATA2LSB
+  Type:            ET_EXEC
+  Machine:         EM_X86_64
+Sections:
+  - Name:            .text
+    Type:            SHT_PROGBITS
+    Flags:           [ SHF_ALLOC, SHF_EXECINSTR ]
+    AddressAlign:    0x1000
+    Size:            24
+  - Name:            .text2
+    Type:            SHT_PROGBITS
+    Flags:           [ SHF_ALLOC, SHF_EXECINSTR ]
+    AddressAlign:    0x10
+    Size:            16
+ProgramHeaders:
+  - Type: PT_LOAD
+    Flags: [ PF_X, PF_R ]
+    Sections:
+      - Section: .text
+  - Type: PT_LOAD
+    Flags: [ PF_X, PF_R ]
+    Sections:
+      - Section: .text2
+
+#CHECK:     ProgramHeaders [
+#CHECK-NEXT:  ProgramHeader {
+#CHECK-NEXT:    Type: PT_LOAD (0x1)
+#CHECK-NEXT:    Offset: 0x1000
+#CHECK-NEXT:    VirtualAddress: 0x0
+#CHECK-NEXT:    PhysicalAddress: 0x0
+#CHECK-NEXT:    FileSize: 24
+#CHECK-NEXT:    MemSize: 24
+#CHECK-NEXT:    Flags [ (0x5)
+#CHECK-NEXT:      PF_R (0x4)
+#CHECK-NEXT:      PF_X (0x1)
+#CHECK-NEXT:    ]
+#CHECK-NEXT:    Alignment: 4096
+#CHECK-NEXT:  }
+#CHECK-NEXT:  ProgramHeader {
+#CHECK-NEXT:    Type: PT_LOAD (0x1)
+#CHECK-NEXT:    Offset: 0x1020
+#CHECK-NEXT:    VirtualAddress: 0x0
+#CHECK-NEXT:    PhysicalAddress: 0x0
+#CHECK-NEXT:    FileSize: 16
+#CHECK-NEXT:    MemSize: 16
+#CHECK-NEXT:    Flags [ (0x5)
+#CHECK-NEXT:      PF_R (0x4)
+#CHECK-NEXT:      PF_X (0x1)
+#CHECK-NEXT:    ]
+#CHECK-NEXT:    Alignment: 16
+#CHECK-NEXT:  }
+#CHECK-NEXT:]
Index: test/tools/llvm-objcopy/identical-segments.test
===================================================================
--- /dev/null
+++ test/tools/llvm-objcopy/identical-segments.test
@@ -0,0 +1,82 @@
+# This test tests that if two possible parent segments have the same offset that
+# they're disambiguated based on their original index. This ensures that cycles
+# do not occur.
+
+# RUN: yaml2obj %s -o %t
+# RUN: llvm-objcopy %t %t2
+# RUN: llvm-readobj --program-headers %t2 | FileCheck %s
+
+!ELF
+FileHeader:
+  Class:           ELFCLASS64
+  Data:            ELFDATA2LSB
+  Type:            ET_EXEC
+  Machine:         EM_X86_64
+Sections:
+  - Name:            .text
+    Type:            SHT_PROGBITS
+    Flags:           [ SHF_ALLOC, SHF_EXECINSTR ]
+    AddressAlign:    0x1000
+    Size:            4096
+  - Name:            .text2
+    Type:            SHT_PROGBITS
+    Flags:           [ SHF_ALLOC, SHF_EXECINSTR ]
+    AddressAlign:    0x1000
+    Size:            4096
+ProgramHeaders:
+  - Type: PT_LOAD
+    Flags: [ PF_X, PF_R ]
+    Sections:
+      - Section: .text2
+  - Type: PT_LOAD
+    Flags: [ PF_X, PF_R ]
+    Sections:
+      - Section: .text
+      - Section: .text2
+  - Type: PT_LOAD
+    Flags: [ PF_X, PF_R ]
+    Sections:
+      - Section: .text
+      - Section: .text2
+
+#CHECK:     ProgramHeaders [
+#CHECK-NEXT:  ProgramHeader {
+#CHECK-NEXT:    Type: PT_LOAD (0x1)
+#CHECK-NEXT:    Offset: 0x2000
+#CHECK-NEXT:    VirtualAddress: 0x0
+#CHECK-NEXT:    PhysicalAddress: 0x0
+#CHECK-NEXT:    FileSize: 4096
+#CHECK-NEXT:    MemSize: 4096
+#CHECK-NEXT:    Flags [ (0x5)
+#CHECK-NEXT:      PF_R (0x4)
+#CHECK-NEXT:      PF_X (0x1)
+#CHECK-NEXT:    ]
+#CHECK-NEXT:    Alignment: 4096
+#CHECK-NEXT:  }
+#CHECK-NEXT:  ProgramHeader {
+#CHECK-NEXT:    Type: PT_LOAD (0x1)
+#CHECK-NEXT:    Offset: 0x1000
+#CHECK-NEXT:    VirtualAddress: 0x0
+#CHECK-NEXT:    PhysicalAddress: 0x0
+#CHECK-NEXT:    FileSize: 8192
+#CHECK-NEXT:    MemSize: 8192
+#CHECK-NEXT:    Flags [ (0x5)
+#CHECK-NEXT:      PF_R (0x4)
+#CHECK-NEXT:      PF_X (0x1)
+#CHECK-NEXT:    ]
+#CHECK-NEXT:    Alignment: 4096
+#CHECK-NEXT:  }
+#CHECK-NEXT:  ProgramHeader {
+#CHECK-NEXT:    Type: PT_LOAD (0x1)
+#CHECK-NEXT:    Offset: 0x1000
+#CHECK-NEXT:    VirtualAddress: 0x0
+#CHECK-NEXT:    PhysicalAddress: 0x0
+#CHECK-NEXT:    FileSize: 8192
+#CHECK-NEXT:    MemSize: 8192
+#CHECK-NEXT:    Flags [ (0x5)
+#CHECK-NEXT:      PF_R (0x4)
+#CHECK-NEXT:      PF_X (0x1)
+#CHECK-NEXT:    ]
+#CHECK-NEXT:    Alignment: 4096
+#CHECK-NEXT:  }
+#CHECK-NEXT:]
Index: test/tools/llvm-objcopy/overlap-chain.test
===================================================================
--- /dev/null
+++ test/tools/llvm-objcopy/overlap-chain.test
@@ -0,0 +1,117 @@
+# This test tests how ParentSegment is set for Segments. In particular this test
+# tests that if a chain of parents forms, the offsets are chosen for parents
+# first despite the order of the list. It also tests multiple branches of the
+# code that assigns parents.
+
+# RUN: yaml2obj %s -o %t
+# RUN: llvm-objcopy %t %t2
+# RUN: llvm-readobj -program-headers %t2 | FileCheck %s
+
+!ELF
+FileHeader:
+  Class:           ELFCLASS64
+  Data:            ELFDATA2LSB
+  Type:            ET_EXEC
+  Machine:         EM_X86_64
+Sections:
+  - Name:            .text
+    Type:            SHT_PROGBITS
+    Flags:           [ SHF_ALLOC, SHF_EXECINSTR ]
+    AddressAlign:    0x1000
+    Size:            4096
+  - Name:            .text2
+    Type:            SHT_PROGBITS
+    Flags:           [ SHF_ALLOC, SHF_EXECINSTR ]
+    AddressAlign:    0x1000
+    Size:            4096
+  - Name:            .text3
+    Type:            SHT_PROGBITS
+    Flags:           [ SHF_ALLOC, SHF_EXECINSTR ]
+    AddressAlign:    0x1000
+    Size:            4096
+  - Name:            .text4
+    Type:            SHT_PROGBITS
+    Flags:           [ SHF_ALLOC, SHF_EXECINSTR ]
+    AddressAlign:    0x1000
+    Size:            4096
+  - Name:            .text5
+    Type:            SHT_PROGBITS
+    Flags:           [ SHF_ALLOC, SHF_EXECINSTR ]
+    AddressAlign:    0x1000
+    Size:            4096
+ProgramHeaders:
+  - Type: PT_LOAD
+    Flags: [ PF_X, PF_R ]
+    Sections:
+      - Section: .text
+      - Section: .text2
+  - Type: PT_LOAD
+    Flags: [ PF_X, PF_R ]
+    Sections:
+      - Section: .text4
+      - Section: .text5
+  - Type: PT_LOAD
+    Flags: [ PF_X, PF_R ]
+    Sections:
+      - Section: .text3
+      - Section: .text4
+  - Type: PT_LOAD
+    Flags: [ PF_X, PF_R ]
+    Sections:
+      - Section: .text2
+      - Section: .text3
+
+#CHECK:     ProgramHeaders [
+#CHECK-NEXT:  ProgramHeader {
+#CHECK-NEXT:    Type: PT_LOAD (0x1)
+#CHECK-NEXT:    Offset: 0x1000
+#CHECK-NEXT:    VirtualAddress: 0x0
+#CHECK-NEXT:    PhysicalAddress: 0x0
+#CHECK-NEXT:    FileSize: 8192
+#CHECK-NEXT:    MemSize: 8192
+#CHECK-NEXT:    Flags [ (0x5)
+#CHECK-NEXT:      PF_R (0x4)
+#CHECK-NEXT:      PF_X (0x1)
+#CHECK-NEXT:    ]
+#CHECK-NEXT:    Alignment: 4096
+#CHECK-NEXT:  }
+#CHECK-NEXT:  ProgramHeader {
+#CHECK-NEXT:    Type: PT_LOAD (0x1)
+#CHECK-NEXT:    Offset: 0x4000
+#CHECK-NEXT:    VirtualAddress: 0x0
+#CHECK-NEXT:    PhysicalAddress: 0x0
+#CHECK-NEXT:    FileSize: 8192
+#CHECK-NEXT:    MemSize: 8192
+#CHECK-NEXT:    Flags [ (0x5)
+#CHECK-NEXT:      PF_R (0x4)
+#CHECK-NEXT:      PF_X (0x1)
+#CHECK-NEXT:    ]
+#CHECK-NEXT:    Alignment: 4096
+#CHECK-NEXT:  }
+#CHECK-NEXT:  ProgramHeader {
+#CHECK-NEXT:    Type: PT_LOAD (0x1)
+#CHECK-NEXT:    Offset: 0x3000
+#CHECK-NEXT:    VirtualAddress: 0x0
+#CHECK-NEXT:    PhysicalAddress: 0x0
+#CHECK-NEXT:    FileSize: 8192
+#CHECK-NEXT:    MemSize: 8192
+#CHECK-NEXT:    Flags [ (0x5)
+#CHECK-NEXT:      PF_R (0x4)
+#CHECK-NEXT:      PF_X (0x1)
+#CHECK-NEXT:    ]
+#CHECK-NEXT:    Alignment: 4096
+#CHECK-NEXT:  }
+#CHECK-NEXT:  ProgramHeader {
+#CHECK-NEXT:    Type: PT_LOAD (0x1)
+#CHECK-NEXT:    Offset: 0x2000
+#CHECK-NEXT:    VirtualAddress: 0x0
+#CHECK-NEXT:    PhysicalAddress: 0x0
+#CHECK-NEXT:    FileSize: 8192
+#CHECK-NEXT:    MemSize: 8192
+#CHECK-NEXT:    Flags [ (0x5)
+#CHECK-NEXT:      PF_R (0x4)
+#CHECK-NEXT:      PF_X (0x1)
+#CHECK-NEXT:    ]
+#CHECK-NEXT:    Alignment: 4096
+#CHECK-NEXT:  }
+#CHECK-NEXT:]
Index: test/tools/llvm-objcopy/pt-phdr.test
===================================================================
--- /dev/null
+++ test/tools/llvm-objcopy/pt-phdr.test
@@ -0,0 +1,71 @@
+# This test simply tests a simple but common real world example of overlapping
+# segments.
+
+# RUN: llvm-objcopy %p/Inputs/pt-phdr.elf %t
+# RUN: llvm-readobj -program-headers %t | FileCheck %s
+
+#CHECK: ProgramHeaders [
+#CHECK-NEXT:  ProgramHeader {
+#CHECK-NEXT:    Type: PT_PHDR
+#CHECK-NEXT:    Offset: 0x40
+#CHECK-NEXT:    VirtualAddress: 0x200040
+#CHECK-NEXT:    PhysicalAddress: 0x200040
+#CHECK-NEXT:    FileSize: 280
+#CHECK-NEXT:    MemSize: 280
+#CHECK-NEXT:    Flags [
+#CHECK-NEXT:      PF_R
+#CHECK-NEXT:    ]
+#CHECK-NEXT:    Alignment: 8
+#CHECK-NEXT:  }
+#CHECK-NEXT:  ProgramHeader {
+#CHECK-NEXT:    Type: PT_LOAD
+#CHECK-NEXT:    Offset: 0x0
+#CHECK-NEXT:    VirtualAddress: 0x200000
+#CHECK-NEXT:    PhysicalAddress: 0x200000
+#CHECK-NEXT:    FileSize: 344
+#CHECK-NEXT:    MemSize: 344
+#CHECK-NEXT:    Flags [
+#CHECK-NEXT:      PF_R
+#CHECK-NEXT:    ]
+#CHECK-NEXT:    Alignment: 4096
+#CHECK-NEXT:  }
+#CHECK-NEXT:  ProgramHeader {
+#CHECK-NEXT:    Type: PT_LOAD
+#CHECK-NEXT:    Offset: 0x1000
+#CHECK-NEXT:    VirtualAddress: 0x201000
+#CHECK-NEXT:    PhysicalAddress: 0x201000
+#CHECK-NEXT:    FileSize: 1
+#CHECK-NEXT:    MemSize: 1
+#CHECK-NEXT:    Flags [
+#CHECK-NEXT:      PF_R
+#CHECK-NEXT:      PF_X
+#CHECK-NEXT:    ]
+#CHECK-NEXT:    Alignment: 4096
+#CHECK-NEXT:  }
+#CHECK-NEXT:  ProgramHeader {
+#CHECK-NEXT:    Type: PT_LOAD
+#CHECK-NEXT:    Offset: 0x2000
+#CHECK-NEXT:    VirtualAddress: 0x202000
+#CHECK-NEXT:    PhysicalAddress: 0x202000
+#CHECK-NEXT:    FileSize: 14
+#CHECK-NEXT:    MemSize: 14
+#CHECK-NEXT:    Flags [
+#CHECK-NEXT:      PF_R
+#CHECK-NEXT:      PF_W
+#CHECK-NEXT:    ]
+#CHECK-NEXT:    Alignment: 4096
+#CHECK-NEXT:  }
+#CHECK-NEXT:  ProgramHeader {
+#CHECK-NEXT:    Type: PT_GNU_STACK (0x6474E551)
+#CHECK-NEXT:    Offset: 0x0
+#CHECK-NEXT:    VirtualAddress: 0x0
+#CHECK-NEXT:    PhysicalAddress: 0x0
+#CHECK-NEXT:    FileSize: 0
+#CHECK-NEXT:    MemSize: 0
+#CHECK-NEXT:    Flags [
+#CHECK-NEXT:      PF_R
+#CHECK-NEXT:      PF_W
+#CHECK-NEXT:    ]
+#CHECK-NEXT:    Alignment: 0
+#CHECK-NEXT:  }
+#CHECK-NEXT:]
Index: test/tools/llvm-objcopy/triple-overlap.test
===================================================================
--- /dev/null
+++ test/tools/llvm-objcopy/triple-overlap.test
@@ -0,0 +1,123 @@
+# This test tests that each segment is assigned a canonical parent segment.
+# Importantly if two segments could be the parent segment of a segment this test
+# should cover the case where a new parent replaces the old parent and the case
+# where an old parent is not replaced by a new parent.
+
+# RUN: yaml2obj %s -o %t
+# RUN: llvm-objcopy %t %t2
+# RUN: llvm-readobj --program-headers %t2 | FileCheck %s
+
+!ELF
+FileHeader:
+  Class:           ELFCLASS64
+  Data:            ELFDATA2LSB
+  Type:            ET_EXEC
+  Machine:         EM_X86_64
+Sections:
+  - Name:            .text
+    Type:            SHT_PROGBITS
+    Flags:           [ SHF_ALLOC, SHF_EXECINSTR ]
+    AddressAlign:    0x1000
+    Size:            4096
+  - Name:            .text2
+    Type:            SHT_PROGBITS
+    Flags:           [ SHF_ALLOC, SHF_EXECINSTR ]
+    AddressAlign:    0x1000
+    Size:            4096
+  - Name:            .text3
+    Type:            SHT_PROGBITS
+    Flags:           [ SHF_ALLOC, SHF_EXECINSTR ]
+    AddressAlign:    0x1000
+    Size:            4096
+  - Name:            .text4
+    Type:            SHT_PROGBITS
+    Flags:           [ SHF_ALLOC, SHF_EXECINSTR ]
+    AddressAlign:    0x1000
+    Size:            4096
+  - Name:            .text5
+    Type:            SHT_PROGBITS
+    Flags:           [ SHF_ALLOC, SHF_EXECINSTR ]
+    AddressAlign:    0x1000
+    Size:            4096
+ProgramHeaders:
+  - Type: PT_LOAD
+    Flags: [ PF_X, PF_R ]
+    Sections:
+      - Section: .text4
+      - Section: .text5
+  - Type: PT_LOAD
+    Flags: [ PF_X, PF_R ]
+    Sections:
+      - Section: .text3
+      - Section: .text4
+      - Section: .text5
+  - Type: PT_LOAD
+    Flags: [ PF_X, PF_R ]
+    Sections:
+      - Section: .text
+      - Section: .text2
+      - Section: .text3
+      - Section: .text4
+      - Section: .text5
+  - Type: PT_LOAD
+    Flags: [ PF_X, PF_R ]
+    Sections:
+      - Section: .text2
+      - Section: .text3
+      - Section: .text4
+      - Section: .text5
+
+#CHECK:     ProgramHeaders [
+#CHECK-NEXT:  ProgramHeader {
+#CHECK-NEXT:    Type: PT_LOAD (0x1)
+#CHECK-NEXT:    Offset: 0x4000
+#CHECK-NEXT:    VirtualAddress: 0x0
+#CHECK-NEXT:    PhysicalAddress: 0x0
+#CHECK-NEXT:    FileSize: 8192
+#CHECK-NEXT:    MemSize: 8192
+#CHECK-NEXT:    Flags [ (0x5)
+#CHECK-NEXT:      PF_R (0x4)
+#CHECK-NEXT:      PF_X (0x1)
+#CHECK-NEXT:    ]
+#CHECK-NEXT:    Alignment: 4096
+#CHECK-NEXT:  }
+#CHECK-NEXT:  ProgramHeader {
+#CHECK-NEXT:    Type: PT_LOAD (0x1)
+#CHECK-NEXT:    Offset: 0x3000
+#CHECK-NEXT:    VirtualAddress: 0x0
+#CHECK-NEXT:    PhysicalAddress: 0x0
+#CHECK-NEXT:    FileSize: 12288
+#CHECK-NEXT:    MemSize: 12288
+#CHECK-NEXT:    Flags [ (0x5)
+#CHECK-NEXT:      PF_R (0x4)
+#CHECK-NEXT:      PF_X (0x1)
+#CHECK-NEXT:    ]
+#CHECK-NEXT:    Alignment: 4096
+#CHECK-NEXT:  }
+#CHECK-NEXT:  ProgramHeader {
+#CHECK-NEXT:    Type: PT_LOAD (0x1)
+#CHECK-NEXT:    Offset: 0x1000
+#CHECK-NEXT:    VirtualAddress: 0x0
+#CHECK-NEXT:    PhysicalAddress: 0x0
+#CHECK-NEXT:    FileSize: 20480
+#CHECK-NEXT:    MemSize: 20480
+#CHECK-NEXT:    Flags [ (0x5)
+#CHECK-NEXT:      PF_R (0x4)
+#CHECK-NEXT:      PF_X (0x1)
+#CHECK-NEXT:    ]
+#CHECK-NEXT:    Alignment: 4096
+#CHECK-NEXT:  }
+#CHECK-NEXT:  ProgramHeader {
+#CHECK-NEXT:    Type: PT_LOAD (0x1)
+#CHECK-NEXT:    Offset: 0x2000
+#CHECK-NEXT:    VirtualAddress: 0x0
+#CHECK-NEXT:    PhysicalAddress: 0x0
+#CHECK-NEXT:    FileSize: 16384
+#CHECK-NEXT:    MemSize: 16384
+#CHECK-NEXT:    Flags [ (0x5)
+#CHECK-NEXT:      PF_R (0x4)
+#CHECK-NEXT:      PF_X (0x1)
+#CHECK-NEXT:    ]
+#CHECK-NEXT:    Alignment: 4096
+#CHECK-NEXT:  }
+#CHECK-NEXT:]
Index: tools/llvm-objcopy/Object.h
===================================================================
--- tools/llvm-objcopy/Object.h
+++ tools/llvm-objcopy/Object.h
@@ -72,6 +72,7 @@
   uint64_t VAddr;
 
   uint64_t OriginalOffset;
+  Segment *ParentSegment;
 
   Segment(llvm::ArrayRef<uint8_t> Data) : Contents(Data) {}
   void finalize();
Index: tools/llvm-objcopy/Object.cpp
===================================================================
--- tools/llvm-objcopy/Object.cpp
+++ tools/llvm-objcopy/Object.cpp
@@ -236,6 +236,15 @@
          Segment.Offset + Segment.FileSize >= Section.OriginalOffset + SecSize;
 }
 
+// Returns true IFF a segment's original offset is inside of another segment's
+// range.
+static bool segmentOverlapsSegment(const Segment &Child,
+                                   const Segment &Parent) {
+
+  return Parent.OriginalOffset <= Child.OriginalOffset &&
+         Parent.OriginalOffset + Parent.FileSize > Child.OriginalOffset;
+}
+
 template <class ELFT>
 void Object<ELFT>::readProgramHeaders(const ELFFile<ELFT> &ElfFile) {
   uint32_t Index = 0;
@@ -254,6 +263,10 @@
     Seg.MemSize = Phdr.p_memsz;
     Seg.Align = Phdr.p_align;
     Seg.Index = Index++;
+    if (Seg.FileSize > Seg.MemSize) {
+      error("Program header at index " + Twine(Seg.Index) +
+              " has p_filesz > p_memsz which is invalid.");
+    }
     for (auto &Section : Sections) {
       if (sectionWithinSegment(*Section, Seg)) {
         Seg.addSection(&*Section);
@@ -264,6 +277,30 @@
       }
     }
   }
+  // Now we do an O(n^2) loop through the segments in order to match up
+  // segments.
+  for (auto &Child : Segments) {
+    for (auto &Parent : Segments) {
+      // Every segment will overlap with itself but we don't want a segment to
+      // be it's own parent so we avoid that situation.
+      if (&Child != &Parent && segmentOverlapsSegment(*Child, *Parent)) {
+        // We want a canonical "most parental" segment but this requires
+        // inspecting the ParentSegment.
+        if (Child->ParentSegment != nullptr) {
+          if (Child->ParentSegment->OriginalOffset > Parent->OriginalOffset) {
+            Child->ParentSegment = Parent.get();
+          } else if (Child->ParentSegment->Index > Parent->Index) {
+            // They must have equal OriginalOffsets so we need to disambiguate.
+            // To decide which is the parent we'll choose the one with the
+            // higher index.
+            Child->ParentSegment = Parent.get();
+          }
+        } else {
+          Child->ParentSegment = Parent.get();
+        }
+      }
+    }
+  }
 }
 
 template <class ELFT>
@@ -493,13 +530,30 @@
 }
 
 template <class ELFT> void ELFObject<ELFT>::assignOffsets() {
+  // We need a temporary list of segments that has a special order to it
+  // so that we know that anytime ->ParentSegment is set that segment has
+  // already had it's offset properly set.
+  std::vector<Segment *> OrderedSegments;
+  for (auto &Segment : this->Segments)
+    OrderedSegments.push_back(Segment.get());
+  auto CompareSegments = [](const Segment *A, const Segment *B) {
+    // Any segment without a parent segment should come before a segment
+    // that has a parent segment.
+    if (A->OriginalOffset < B->OriginalOffset)
+      return true;
+    if (A->OriginalOffset > B->OriginalOffset)
+      return false;
+    return A->Index < B->Index;
+  };
+  std::stable_sort(std::begin(OrderedSegments), std::end(OrderedSegments),
+                   CompareSegments);
   // The size of ELF + program headers will not change so it is ok to assume
   // that the first offset of the first segment is a good place to start
   // outputting sections. This covers both the standard case and the PT_PHDR
   // case.
   uint64_t Offset;
-  if (!this->Segments.empty()) {
-    Offset = this->Segments[0]->Offset;
+  if (!OrderedSegments.empty()) {
+    Offset = OrderedSegments[0]->Offset;
   } else {
     Offset = sizeof(Elf_Ehdr);
   }
@@ -508,10 +562,22 @@
   // then it's acceptable, but not ideal, to simply move it to after the
   // segments. So we can simply layout segments one after the other accounting
   // for alignment.
-  for (auto &Segment : this->Segments) {
-    Offset = alignTo(Offset, Segment->Align);
-    Segment->Offset = Offset;
-    Offset += Segment->FileSize;
+  for (auto &Segment : OrderedSegments) {
+    if (Segment->OriginalOffset == 0 && Segment->MemSize == 0)
+      continue;
+    // We assume that segments have been ordered by OriginalOffset and Index
+    // such that a parent segment will always come before a child segment in
+    // OrderedSegments. This means that the Offset of the ParentSegment should
+    // already be set and we can set our offset relative to it.
+    if (Segment->ParentSegment != nullptr) {
+      auto Parent = Segment->ParentSegment;
+      Segment->Offset =
+          Parent->Offset + Segment->OriginalOffset - Parent->OriginalOffset;
+    } else {
+      Offset = alignTo(Offset, Segment->Align);
+      Segment->Offset = Offset;
+      Offset += Segment->FileSize;
+    }
   }
   // Now the offset of every segment has been set we can assign the offsets
   // of each section. For sections that are covered by a segment we should use