MANTA-1483 Update htslib/samtools to 1.9

This update is motivated by a possible CRAM-specfic memory issue
suggested by Illumina#154

Author: ctsa

COPYRIGHT.txt

@@ -26,7 +26,7 @@ library:
 
 ******************************************************************
 
-htslib 1.7-6-g6d2bfb7
+htslib 1.9
 
 [Files in this distribution outwith the cram/ subdirectory are distributed
 according to the terms of the following MIT/Expat license.]
@@ -103,7 +103,7 @@ to a notice that reads "Copyright (C) 2005, 2006, 2007, 2008, 2009, 2010,
 
 ******************************************************************
 
-samtools 1.6
+samtools 1.9
 
 The MIT/Expat License
 

redist/CMakeLists.txt

@@ -71,7 +71,7 @@ superset(CTPL_DIR "${THIS_REDIST_DIR}/${CTPL_PREFIX}")
 #
 # htslib
 #
-set(HTSLIB_PREFIX "htslib-1.7-6-g6d2bfb7")
+set(HTSLIB_PREFIX "htslib-1.9")
 superset(HTSLIB_DIR "${CMAKE_CURRENT_BINARY_DIR}/${HTSLIB_PREFIX}")
 superset(HTSLIB_LIBRARY "${HTSLIB_DIR}/libhts.a")
 
@@ -117,7 +117,7 @@ endif ()
 #
 # samtools
 #
-set(SAMTOOLS_PREFIX "samtools-1.6")
+set(SAMTOOLS_PREFIX "samtools-1.9")
 set(SAMTOOLS_DIR "${CMAKE_CURRENT_BINARY_DIR}/${SAMTOOLS_PREFIX}")
 set(SAMTOOLS_LIBRARY "${SAMTOOLS_DIR}/libbam.a")
 superset(SAMTOOLS_PROG "${SAMTOOLS_DIR}/samtools")

redist/README.md

@@ -17,10 +17,6 @@ To reduce size, both packages have been modified to remove the test
 directories and test references in the makefiles. The copy of htslib
 in samtools has been removed.
 
-Note that an off-release htslib version is used here because the fix to
-issue https://github.com/samtools/htslib/issues/654 is required for
-valid analysis from alignments in CRAM format.
-
 ### cmake-modules
 
 cmake-modules-c99fd3 modified to show git describe --dirty