diff --git a/configure.ac b/configure.ac
index 73f7a2c2f..d860a74fe 100644
--- a/configure.ac
+++ b/configure.ac
@@ -326,7 +326,7 @@ HTS_HIDE_DYNAMIC_SYMBOLS
 
 dnl FIXME This pulls in dozens of standard header checks
 AC_FUNC_MMAP
-AC_CHECK_FUNCS([gmtime_r fsync drand48 srand48_deterministic getauxval elf_aux_info])
+AC_CHECK_FUNCS([gmtime_r fsync drand48 srand48_deterministic getauxval elf_aux_info posix_memalign])
 
 # Darwin has a dubious fdatasync() symbol, but no declaration in <unistd.h>
 AC_CHECK_DECL([fdatasync(int)], [AC_CHECK_FUNCS(fdatasync)])
diff --git a/hfile.c b/hfile.c
index 552b71774..3b60bedda 100644
--- a/hfile.c
+++ b/hfile.c
@@ -107,12 +107,20 @@ hFILE *hfile_init(size_t struct_size, const char *mode, size_t capacity)
     hFILE *fp = (hFILE *) malloc(struct_size);
     if (fp == NULL) goto error;
 
-    if (capacity == 0) capacity = 32768;
+    const int maxcap = 128*1024;
+
+    if (capacity == 0) capacity = maxcap;
     // FIXME For now, clamp input buffer sizes so mpileup doesn't eat memory
-    if (strchr(mode, 'r') && capacity > 32768) capacity = 32768;
+    if (strchr(mode, 'r') && capacity > maxcap) capacity = maxcap;
 
+#ifdef HAVE_POSIX_MEMALIGN
+    fp->buffer = NULL;
+    if (posix_memalign((void **)&fp->buffer, 256, capacity) < 0)
+        goto error;
+#else
     fp->buffer = (char *) malloc(capacity);
     if (fp->buffer == NULL) goto error;
+#endif
 
     fp->begin = fp->end = fp->buffer;
     fp->limit = &fp->buffer[capacity];
@@ -629,7 +637,12 @@ static size_t blksize(int fd)
 #ifdef HAVE_STRUCT_STAT_ST_BLKSIZE
     struct stat sbuf;
     if (fstat(fd, &sbuf) != 0) return 0;
-    return sbuf.st_blksize;
+
+    // Pipes/FIFOs on linux return 4Kb here often, but it's much too small
+    // for performant I/O.
+    return S_ISFIFO(sbuf.st_mode)
+        ? 128*1024
+        : sbuf.st_blksize;
 #else
     return 0;
 #endif