From f40e38b57547c01f64ae877d4d82c789a8271791 Mon Sep 17 00:00:00 2001
From: John Marshall <jmarshall@hey.com>
Date: Wed, 10 Feb 2021 08:54:51 +0000
Subject: [PATCH] Fix sam_view.o dependencies (and other very minor updates)

Add recently-added $(htslib_hts_expr_h) inclusion.
Update .ci_helpers/clone comment. Fix configure.ac typo so
user-specified $CPPFLAGS aren't ignored on MSYS/MinGW.
---
 .ci_helpers/clone | 2 +-
 Makefile          | 2 +-
 configure.ac      | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.ci_helpers/clone b/.ci_helpers/clone
index 7e5cf317a..025001adc 100755
--- a/.ci_helpers/clone
+++ b/.ci_helpers/clone
@@ -1,5 +1,5 @@
 #!/bin/sh
-# Usage: .travis/clone REPOSITORY [DIR] [BRANCH]
+# Usage: .ci_helpers/clone REPOSITORY [DIR] [BRANCH]
 #
 # Creates a shallow clone, checking out the specified branch.  If BRANCH is
 # omitted or if there is no branch with that name, checks out origin/HEAD
diff --git a/Makefile b/Makefile
index 8cabc15a1..2f56ee373 100644
--- a/Makefile
+++ b/Makefile
@@ -202,7 +202,7 @@ phase.o: phase.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(
 sam.o: sam.c config.h $(htslib_faidx_h) $(sam_h)
 sam_opts.o: sam_opts.c config.h $(sam_opts_h)
 sam_utils.o: sam_utils.c config.h $(samtools_h)
-sam_view.o: sam_view.c config.h $(htslib_sam_h) $(htslib_faidx_h) $(htslib_khash_h) $(htslib_thread_pool_h) $(samtools_h) $(sam_opts_h) $(bedidx_h)
+sam_view.o: sam_view.c config.h $(htslib_sam_h) $(htslib_faidx_h) $(htslib_khash_h) $(htslib_thread_pool_h) $(htslib_hts_expr_h) $(samtools_h) $(sam_opts_h) $(bedidx_h)
 sample.o: sample.c config.h $(sample_h) $(htslib_khash_h)
 stats_isize.o: stats_isize.c config.h $(stats_isize_h) $(htslib_khash_h)
 stats.o: stats.c config.h $(htslib_faidx_h) $(htslib_sam_h) $(htslib_hts_h) $(htslib_hts_defs_h) $(htslib_khash_str2int_h) $(samtools_h) $(htslib_khash_h) $(htslib_kstring_h) $(stats_isize_h) $(sam_opts_h) $(bedidx_h)
diff --git a/configure.ac b/configure.ac
index cbf057c0d..a1b1a5acc 100644
--- a/configure.ac
+++ b/configure.ac
@@ -137,7 +137,7 @@ case $host_alias in
     # This also sets __USE_MINGW_ANSI_STDIO which in turn makes PRId64,
     # %lld and %z printf formats work.  It also enforces the snprintf to
     # be C99 compliant so it returns the correct values (in kstring.c).
-    CPPFLAGS="$CPPCFLAGS -D_XOPEN_SOURCE=600"
+    CPPFLAGS="$CPPFLAGS -D_XOPEN_SOURCE=600"
     ;;
 esac