Increase the input block size for bgzip.

Commit e495718 changed bgzip from unix raw POSIX read() calls to
hread().  Unfortunately hread gets its buffer size from stat of the
input file descriptor, which can be 4kb for a pipe.  We're reading
0xff00 bytes, so this ends up being split over two reads mostly, with
one or both involving additional memcpys.  This makes the buffered I/O
worse performing than non-buffered.  In the most extreme cases (cat
data | bgzip -l0 > /dev/null) this is a two fold slow down.

The easy solution is just to increase the buffer size to something
sensible.  Currently we play it cautiously and only do this on pipes
and fifos.

Fixes samtools#1767

hfile.c

@@ -107,9 +107,11 @@ 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;
 
     fp->buffer = (char *) malloc(capacity);
     if (fp->buffer == NULL) goto error;
@@ -629,7 +631,12 @@ 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