diff -Nru htslib-1.3/debian/changelog htslib-1.3/debian/changelog
--- htslib-1.3/debian/changelog	2016-02-08 16:50:22.000000000 +0000
+++ htslib-1.3/debian/changelog	2016-02-23 20:41:33.000000000 +0000
@@ -1,3 +1,16 @@
+htslib (1.3-2+rpi1) stretch-staging; urgency=medium
+
+  [changes brought forward from 1.2.1-1+rpi1 by Peter Michael Green <plugwash@raspbian.org> at Tue, 29 Sep 2015 19:03:00 +0000]
+  * Fix bus errors in testsuite.
+  
+  [changes introduced in 1.2.1-2+rpi1 by Peter Michael Green]
+  * Cleanup duplicated patching with one version bad that made it impossible to unpack source package
+    manually.
+  * Remove single-debian-patch from debian/source/options, it was almost certainly responsible for
+    the above source package screwup.
+
+ -- Raspbian forward porter <root@raspbian.org>  Tue, 23 Feb 2016 20:41:33 +0000
+
 htslib (1.3-2) unstable; urgency=medium
 
   * Team upload
diff -Nru htslib-1.3/debian/patches/alignment.patch htslib-1.3/debian/patches/alignment.patch
--- htslib-1.3/debian/patches/alignment.patch	1970-01-01 00:00:00.000000000 +0000
+++ htslib-1.3/debian/patches/alignment.patch	2016-02-23 20:41:33.000000000 +0000
@@ -0,0 +1,119 @@
+Description: Fix alignment issues
+ Fix alignment issues identified through test failure with "BUS error" when
+ building on Debian armhf and raspbian.
+Author: Peter Michael Green <plugwash@raspbian.org>
+
+---
+The information above should follow the Patch Tagging Guidelines, please
+checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
+are templates for supplementary fields that you might want to add:
+
+Origin: <vendor|upstream|other>, <url of original patch>
+Bug: <url in upstream bugtracker>
+Bug-Debian: https://bugs.debian.org/<bugnumber>
+Bug-Ubuntu: https://launchpad.net/bugs/<bugnumber>
+Forwarded: <no|not-needed|url proving that it has been forwarded>
+Reviewed-By: <name and email of someone who approved the patch>
+Last-Update: <YYYY-MM-DD>
+
+Index: htslib-1.3/sam.c
+===================================================================
+--- htslib-1.3.orig/sam.c
++++ htslib-1.3/sam.c
+@@ -1056,6 +1056,12 @@ err_recover:
+     }
+ }
+ 
++#define READUNALIGNED(ptr,type) ({ \
++    type tmp;\
++    memcpy(&tmp,ptr,sizeof(type));\
++    tmp;\
++})
++
+ int sam_format1(const bam_hdr_t *h, const bam1_t *b, kstring_t *str)
+ {
+     int i;
+@@ -1119,36 +1125,36 @@ int sam_format1(const bam_hdr_t *h, cons
+         } else if (type == 'S') {
+             if (s+2 <= b->data + b->l_data) {
+                 kputsn("i:", 2, str);
+-                kputw(*(uint16_t*)s, str);
++                kputw(READUNALIGNED(s,uint16_t), str);
+                 s += 2;
+             } else return -1;
+         } else if (type == 's') {
+             if (s+2 <= b->data + b->l_data) {
+                 kputsn("i:", 2, str);
+-                kputw(*(int16_t*)s, str);
++                kputw(READUNALIGNED(s,int16_t), str);
+                 s += 2;
+             } else return -1;
+         } else if (type == 'I') {
+             if (s+4 <= b->data + b->l_data) {
+                 kputsn("i:", 2, str);
+-                kputuw(*(uint32_t*)s, str);
++                kputuw(READUNALIGNED(s,uint32_t), str);
+                 s += 4;
+             } else return -1;
+         } else if (type == 'i') {
+             if (s+4 <= b->data + b->l_data) {
+                 kputsn("i:", 2, str);
+-                kputw(*(int32_t*)s, str);
++                kputw(READUNALIGNED(s,int32_t), str);
+                 s += 4;
+             } else return -1;
+         } else if (type == 'f') {
+             if (s+4 <= b->data + b->l_data) {
+-                ksprintf(str, "f:%g", *(float*)s);
++                ksprintf(str, "f:%g", READUNALIGNED(s,float));
+                 s += 4;
+             } else return -1;
+ 
+         } else if (type == 'd') {
+             if (s+8 <= b->data + b->l_data) {
+-                ksprintf(str, "d:%g", *(double*)s);
++                ksprintf(str, "d:%g", READUNALIGNED(s,double));
+                 s += 8;
+             } else return -1;
+         } else if (type == 'Z' || type == 'H') {
+@@ -1172,11 +1178,11 @@ int sam_format1(const bam_hdr_t *h, cons
+                 kputc(',', str);
+                 if ('c' == sub_type)      { kputw(*(int8_t*)s, str); ++s; }
+                 else if ('C' == sub_type) { kputw(*(uint8_t*)s, str); ++s; }
+-                else if ('s' == sub_type) { kputw(*(int16_t*)s, str); s += 2; }
+-                else if ('S' == sub_type) { kputw(*(uint16_t*)s, str); s += 2; }
+-                else if ('i' == sub_type) { kputw(*(int32_t*)s, str); s += 4; }
+-                else if ('I' == sub_type) { kputuw(*(uint32_t*)s, str); s += 4; }
+-                else if ('f' == sub_type) { ksprintf(str, "%g", *(float*)s); s += 4; }
++                else if ('s' == sub_type) { kputw(READUNALIGNED(s,int16_t), str); s += 2; }
++                else if ('S' == sub_type) { kputw(READUNALIGNED(s,uint16_t), str); s += 2; }
++                else if ('i' == sub_type) { kputw(READUNALIGNED(s,int32_t), str); s += 4; }
++                else if ('I' == sub_type) { kputuw(READUNALIGNED(s,uint32_t), str); s += 4; }
++                else if ('f' == sub_type) { ksprintf(str, "%g", READUNALIGNED(s,float)); s += 4; }
+                 else return -1;
+             }
+         }
+@@ -1283,9 +1289,9 @@ int32_t bam_aux2i(const uint8_t *s)
+     type = *s++;
+     if (type == 'c') return (int32_t)*(int8_t*)s;
+     else if (type == 'C') return (int32_t)*(uint8_t*)s;
+-    else if (type == 's') return (int32_t)*(int16_t*)s;
+-    else if (type == 'S') return (int32_t)*(uint16_t*)s;
+-    else if (type == 'i' || type == 'I') return *(int32_t*)s;
++    else if (type == 's') return (int32_t)READUNALIGNED(s,int16_t);
++    else if (type == 'S') return (int32_t)READUNALIGNED(s,uint16_t);
++    else if (type == 'i' || type == 'I') return READUNALIGNED(s,int32_t);
+     else return 0;
+ }
+ 
+@@ -1293,8 +1299,8 @@ double bam_aux2f(const uint8_t *s)
+ {
+     int type;
+     type = *s++;
+-    if (type == 'd') return *(double*)s;
+-    else if (type == 'f') return *(float*)s;
++    if (type == 'd') return READUNALIGNED(s,double);
++    else if (type == 'f') return READUNALIGNED(s,float);
+     else return 0.0;
+ }
+ 
diff -Nru htslib-1.3/debian/patches/series htslib-1.3/debian/patches/series
--- htslib-1.3/debian/patches/series	2016-02-08 16:11:20.000000000 +0000
+++ htslib-1.3/debian/patches/series	2016-02-23 20:41:33.000000000 +0000
@@ -1,3 +1,4 @@
 add_largefile.patch
 define_PATH_MAX.patch
 literal_version.patch
+alignment.patch
diff -Nru htslib-1.3/debian/source/options htslib-1.3/debian/source/options
--- htslib-1.3/debian/source/options	2016-01-30 14:38:57.000000000 +0000
+++ htslib-1.3/debian/source/options	2016-02-23 20:41:33.000000000 +0000
@@ -1,2 +1 @@
-single-debian-patch
 extend-diff-ignore = "^(\.travis\.yml|README.md)$"