[med-svn] [htslib] 01/01: Update 877670.patch as it was applied upstream

[Graham Inggs]

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ginggs pushed a commit to branch debian/unstable
in repository htslib.

commit 5540e882d8b5ab1674f76204da36162f9336b179
Author: Graham Inggs <ginggs at debian.org>
Date:   Fri Nov 10 14:18:42 2017 +0200

    Update 877670.patch as it was applied upstream
---
 debian/changelog            |  4 ++++
 debian/patches/877670.patch | 18 ++++++++++++++----
 2 files changed, 18 insertions(+), 4 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index aced9dd..0aa6304 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,12 @@
 htslib (1.5-3) UNRELEASED; urgency=medium
 
+  [ Diane Trout ]
   * Restore libhts2.symbols and update for changes from 1.4.1 and 1.5
     versions of htslib.
 
+  [ Graham Inggs ]
+  * Update 877670.patch as it was applied upstream
+
  -- Diane Trout <diane at ghic.org>  Fri, 10 Nov 2017 12:38:12 +0100
 
 htslib (1.5-2) unstable; urgency=medium
diff --git a/debian/patches/877670.patch b/debian/patches/877670.patch
index b03f067..82f9f09 100644
--- a/debian/patches/877670.patch
+++ b/debian/patches/877670.patch
@@ -2,11 +2,21 @@ 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 at debian.org>
-Last-Update: 2017-11-08
+Last-Update: 2017-11-10
 --- a/errmod.c
 +++ b/errmod.c
-@@ -82,10 +82,11 @@ static void cal_coef(errmod_t *em, doubl
+@@ -62,7 +62,7 @@
+ 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
+@@ -82,10 +82,11 @@
          double le1 = log(1.0 - e);
          for (n = 1; n <= 255; ++n) {
              double *beta = em->beta + (q<<16|n<<8);
@@ -15,9 +25,9 @@ Last-Update: 2017-11-08
 -                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] = INFINITY;
++            beta[n] = HUGE_VAL;
 +            for (k = n - 1; k >= 0; --k, sum1 = sum) {
-+                sum = sum1 + log1pl(expl(lC[n<<8|k] + k*le + (n-k)*le1 - sum1));
++                sum = sum1 + log1p(exp(lC[n<<8|k] + k*le + (n-k)*le1 - sum1));
 +                beta[k] = -10. / M_LN10 * (sum1 - sum);
              }
          }

-- 
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