debian/changelog

+htslib (1.9-8) unstable; urgency=medium
+
+  * Disable optimization on ppc64el to unblock this and many other packages
+    migration to testing.
+
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Mon, 31 Dec 2018 07:08:13 -0800
+
 htslib (1.9-7) unstable; urgency=medium
 
   * Bring i386 build enhancements to unstable.

debian/control

@@ -12,7 +12,7 @@ Build-Depends: debhelper (>= 11~),
                liblzma-dev,
                libssl-dev,
                zlib1g-dev
-Standards-Version: 4.2.1
+Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/htslib
 Vcs-Git: https://salsa.debian.org/med-team/htslib.git
 Homepage: https://github.com/samtools/htslib
@@ -24,7 +24,8 @@ Section: libs
 Depends: ${misc:Depends},
          ${shlibs:Depends}
 Pre-Depends: ${misc:Pre-Depends}
-Breaks: python-pysam (<< 0.15~), python3-pysam (<< 0.15~)
+Breaks: python-pysam (<< 0.15~),
+        python3-pysam (<< 0.15~)
 Description: C library for high-throughput sequencing data formats
  HTSlib is an implementation of a unified C library for accessing common file
  formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call

debian/patches/877670.patch

-Description: Fix calculation of PLs on ARM and POWER
-Bug: https://github.com/samtools/bcftools/issues/702
-Bug-Debian: https://bugs.debian.org/877670
-Forwarded: https://github.com/samtools/htslib/pull/617
-Applied-Upstream: https://github.com/samtools/htslib/commit/829ddaea433cd55cc5bd9a6d38ec6d9593ad50b4
-Author: Graham Inggs <ginggs@debian.org>
-Last-Update: 2017-11-10
---- a/errmod.c
-+++ b/errmod.c
-@@ -64,7 +64,7 @@ static double* logbinomial_table( const
- static void cal_coef(errmod_t *em, double depcorr, double eta)
- {
-     int k, n, q;
--    long double sum, sum1;
-+    double sum, sum1;
-     double *lC;
- 
-     // initialize ->fk
-@@ -84,10 +84,11 @@ static void cal_coef(errmod_t *em, doubl
-         double le1 = log(1.0 - e);
-         for (n = 1; n <= 255; ++n) {
-             double *beta = em->beta + (q<<16|n<<8);
--            sum1 = sum = 0.0;
--            for (k = n; k >= 0; --k, sum1 = sum) {
--                sum = sum1 + expl(lC[n<<8|k] + k*le + (n-k)*le1);
--                beta[k] = -10. / M_LN10 * logl(sum1 / sum);
-+            sum1 = lC[n<<8|n] + n*le;
-+            beta[n] = HUGE_VAL;
-+            for (k = n - 1; k >= 0; --k, sum1 = sum) {
-+                sum = sum1 + log1p(exp(lC[n<<8|k] + k*le + (n-k)*le1 - sum1));
-+                beta[k] = -10. / M_LN10 * (sum1 - sum);
-             }
-         }
-     }

debian/patches/fix_float_precision

+From: Gustavo Romero <gromero@linux.vnet.ibm.com>
+Subject: ppc64el float handling fix
+
+I dug a bit further and it looks like that sam_parse1() is actually
+generating a different value for the floats in question, so when they are
+loaded back for the comparison they are already screwed up, e.g.:
+
+-- O3 --
+0xc0490fcf
+-3.14158988
+
+-- O0 --
+0xc0490fd0
+-3.14159012 (expected)
+
+because strtod() is used in float_to_le() and so also in u32_to_le(), which are
+inlined and float_to_le() takes a float and not a double as the first argument
+the use strtof() instead of strtod() in there looks the best, avoiding a
+truncation from double to float, which might cause precision issues, specially
+between different archs (like casts) plus optimization. So the following
+change fixed the issue for me.
+
+--- htslib.orig/sam.c
++++ htslib/sam.c
+@@ -1408,7 +1408,7 @@
+             else if (type == 'S') while (q + 1 < p) { u16_to_le(strtoul(q + 1, &q, 0), (uint8_t *) str.s + str.l); str.l += 2; _skip_to_comma(q, p); }
+             else if (type == 'i') while (q + 1 < p) { i32_to_le(strtol(q + 1, &q, 0), (uint8_t *) str.s + str.l); str.l += 4; _skip_to_comma(q, p); }
+             else if (type == 'I') while (q + 1 < p) { u32_to_le(strtoul(q + 1, &q, 0), (uint8_t *) str.s + str.l); str.l += 4; _skip_to_comma(q, p); }
+-            else if (type == 'f') while (q + 1 < p) { float_to_le(strtod(q + 1, &q), (uint8_t *) str.s + str.l); str.l += 4; _skip_to_comma(q, p); }
++            else if (type == 'f') while (q + 1 < p) { float_to_le(strtof(q + 1, &q), (uint8_t *) str.s + str.l); str.l += 4; _skip_to_comma(q, p); }
+             else _parse_err_param(1, "unrecognized type B:%c", type);
+ 
+ #undef _skip_to_comma

debian/patches/series

 define_PATH_MAX.patch
 fPIC.patch
-#877670.patch	# applied by upstream
 testShebang.patch
+#fix_float_precision  # doesn't fix all errors on ppc64el yet

debian/rules

@@ -10,8 +10,15 @@ include /usr/share/dpkg/default.mk
 ifneq (,$(filter $(DEB_HOST_ARCH),i386 kfreebsd-i386 hurd-i386))
   DEB_CFLAGS_MAINT_APPEND=-msse -mfpmath=sse
 endif
-export DEB_CFLAGS_MAINT_APPEND+=-flto
-export DEB_LDFLAGS_MAINT_APPEND+=-Wl,-flto
+ifneq (,$(filter $(DEB_HOST_ARCH),ppc64el))
+  DEB_CFLAGS_MAINT_APPEND+=-O0
+else
+  DEB_CFLAGS_MAINT_APPEND+=-flto
+  DEB_LDFLAGS_MAINT_APPEND+=-Wl,-flto
+endif
+
+export DEB_CFLAGS_MAINT_APPEND
+export DEB_LDFLAGS_MAINT_APPEND
 
 %:
 	dh $@