Browse code

Update gstruct (bam_tally)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@110046 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 28/10/2015 20:55:30
Showing9 changed files

... ...
@@ -12,8 +12,8 @@ without warranty of any kind.
12 12
 Basic Installation
13 13
 ==================
14 14
 
15
-   Briefly, the shell command `./configure && make && make install'
16
-should configure, build, and install this package.  The following
15
+   Briefly, the shell commands `./configure; make; make install' should
16
+configure, build, and install this package.  The following
17 17
 more-detailed instructions are generic; see the `README' file for
18 18
 instructions specific to this package.  Some packages provide this
19 19
 `INSTALL' file but do not implement all of the features documented
... ...
@@ -79,13 +79,13 @@ build_triplet = @build@
79 79
 host_triplet = @host@
80 80
 target_triplet = @target@
81 81
 subdir = .
82
-DIST_COMMON = INSTALL NEWS README AUTHORS ChangeLog \
82
+DIST_COMMON = INSTALL NEWS README AUTHORS ChangeLog COPYING \
83 83
 	$(srcdir)/Makefile.in $(srcdir)/Makefile.am \
84 84
 	$(top_srcdir)/configure $(am__configure_deps) \
85
-	$(top_srcdir)/lib/gstruct.pc.in COPYING config/compile \
86
-	config/config.guess config/config.sub config/depcomp \
87
-	config/install-sh config/missing config/ltmain.sh \
88
-	$(top_srcdir)/config/compile $(top_srcdir)/config/config.guess \
85
+	$(top_srcdir)/lib/gstruct.pc.in config/compile \
86
+	config/config.guess config/config.sub config/install-sh \
87
+	config/missing config/ltmain.sh $(top_srcdir)/config/compile \
88
+	$(top_srcdir)/config/config.guess \
89 89
 	$(top_srcdir)/config/config.sub \
90 90
 	$(top_srcdir)/config/install-sh $(top_srcdir)/config/ltmain.sh \
91 91
 	$(top_srcdir)/config/missing
... ...
@@ -2,7 +2,7 @@
2 2
 # Configuration validation subroutine script.
3 3
 #   Copyright 1992-2013 Free Software Foundation, Inc.
4 4
 
5
-timestamp='2013-08-10'
5
+timestamp='2013-04-24'
6 6
 
7 7
 # This file is free software; you can redistribute it and/or modify it
8 8
 # under the terms of the GNU General Public License as published by
... ...
@@ -257,7 +257,7 @@ case $basic_machine in
257 257
 	| avr | avr32 \
258 258
 	| be32 | be64 \
259 259
 	| bfin \
260
-	| c4x | c8051 | clipper \
260
+	| c4x | clipper \
261 261
 	| d10v | d30v | dlx | dsp16xx \
262 262
 	| epiphany \
263 263
 	| fido | fr30 | frv \
... ...
@@ -372,7 +372,7 @@ case $basic_machine in
372 372
 	| be32-* | be64-* \
373 373
 	| bfin-* | bs2000-* \
374 374
 	| c[123]* | c30-* | [cjt]90-* | c4x-* \
375
-	| c8051-* | clipper-* | craynv-* | cydra-* \
375
+	| clipper-* | craynv-* | cydra-* \
376 376
 	| d10v-* | d30v-* | dlx-* \
377 377
 	| elxsi-* \
378 378
 	| f30[01]-* | f700-* | fido-* | fr30-* | frv-* | fx80-* \
... ...
@@ -794,7 +794,7 @@ case $basic_machine in
794 794
 		os=-mingw64
795 795
 		;;
796 796
 	mingw32)
797
-		basic_machine=i686-pc
797
+		basic_machine=i386-pc
798 798
 		os=-mingw32
799 799
 		;;
800 800
 	mingw32ce)
... ...
@@ -830,7 +830,7 @@ case $basic_machine in
830 830
 		basic_machine=`echo $basic_machine | sed -e 's/ms1-/mt-/'`
831 831
 		;;
832 832
 	msys)
833
-		basic_machine=i686-pc
833
+		basic_machine=i386-pc
834 834
 		os=-msys
835 835
 		;;
836 836
 	mvs)
... ...
@@ -1546,9 +1546,6 @@ case $basic_machine in
1546 1546
 	c4x-* | tic4x-*)
1547 1547
 		os=-coff
1548 1548
 		;;
1549
-	c8051-*)
1550
-		os=-elf
1551
-		;;
1552 1549
 	hexagon-*)
1553 1550
 		os=-elf
1554 1551
 		;;
... ...
@@ -1312,7 +1312,7 @@ ia64-*-hpux*)
1312 1312
   rm -rf conftest*
1313 1313
   ;;
1314 1314
 
1315
-x86_64-*kfreebsd*-gnu|x86_64-*linux*|powerpc*-*linux*| \
1315
+x86_64-*kfreebsd*-gnu|x86_64-*linux*|ppc*-*linux*|powerpc*-*linux*| \
1316 1316
 s390*-*linux*|s390*-*tpf*|sparc*-*linux*)
1317 1317
   # Find out which ABI we are using.
1318 1318
   echo 'int i;' > conftest.$ac_ext
... ...
@@ -1324,19 +1324,9 @@ s390*-*linux*|s390*-*tpf*|sparc*-*linux*)
1324 1324
 	    LD="${LD-ld} -m elf_i386_fbsd"
1325 1325
 	    ;;
1326 1326
 	  x86_64-*linux*)
1327
-	    case `/usr/bin/file conftest.o` in
1328
-	      *x86-64*)
1329
-		LD="${LD-ld} -m elf32_x86_64"
1330
-		;;
1331
-	      *)
1332
-		LD="${LD-ld} -m elf_i386"
1333
-		;;
1334
-	    esac
1335
-	    ;;
1336
-	  powerpc64le-*)
1337
-	    LD="${LD-ld} -m elf32lppclinux"
1327
+	    LD="${LD-ld} -m elf_i386"
1338 1328
 	    ;;
1339
-	  powerpc64-*)
1329
+	  ppc64-*linux*|powerpc64-*linux*)
1340 1330
 	    LD="${LD-ld} -m elf32ppclinux"
1341 1331
 	    ;;
1342 1332
 	  s390x-*linux*)
... ...
@@ -1355,10 +1345,7 @@ s390*-*linux*|s390*-*tpf*|sparc*-*linux*)
1355 1345
 	  x86_64-*linux*)
1356 1346
 	    LD="${LD-ld} -m elf_x86_64"
1357 1347
 	    ;;
1358
-	  powerpcle-*)
1359
-	    LD="${LD-ld} -m elf64lppc"
1360
-	    ;;
1361
-	  powerpc-*)
1348
+	  ppc*-*linux*|powerpc*-*linux*)
1362 1349
 	    LD="${LD-ld} -m elf64ppc"
1363 1350
 	    ;;
1364 1351
 	  s390*-*linux*|s390*-*tpf*)
... ...
@@ -1701,8 +1688,7 @@ AC_CACHE_VAL([lt_cv_sys_max_cmd_len], [dnl
1701 1688
     ;;
1702 1689
   *)
1703 1690
     lt_cv_sys_max_cmd_len=`(getconf ARG_MAX) 2> /dev/null`
1704
-    if test -n "$lt_cv_sys_max_cmd_len" && \
1705
-	test undefined != "$lt_cv_sys_max_cmd_len"; then
1691
+    if test -n "$lt_cv_sys_max_cmd_len"; then
1706 1692
       lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4`
1707 1693
       lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3`
1708 1694
     else
... ...
@@ -2526,6 +2512,17 @@ freebsd* | dragonfly*)
2526 2512
   esac
2527 2513
   ;;
2528 2514
 
2515
+gnu*)
2516
+  version_type=linux # correct to gnu/linux during the next big refactor
2517
+  need_lib_prefix=no
2518
+  need_version=no
2519
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}'
2520
+  soname_spec='${libname}${release}${shared_ext}$major'
2521
+  shlibpath_var=LD_LIBRARY_PATH
2522
+  shlibpath_overrides_runpath=no
2523
+  hardcode_into_libs=yes
2524
+  ;;
2525
+
2529 2526
 haiku*)
2530 2527
   version_type=linux # correct to gnu/linux during the next big refactor
2531 2528
   need_lib_prefix=no
... ...
@@ -2642,7 +2639,7 @@ linux*oldld* | linux*aout* | linux*coff*)
2642 2639
   ;;
2643 2640
 
2644 2641
 # This must be glibc/ELF.
2645
-linux* | k*bsd*-gnu | kopensolaris*-gnu | gnu*)
2642
+linux* | k*bsd*-gnu | kopensolaris*-gnu)
2646 2643
   version_type=linux # correct to gnu/linux during the next big refactor
2647 2644
   need_lib_prefix=no
2648 2645
   need_version=no
... ...
@@ -2687,18 +2684,6 @@ linux* | k*bsd*-gnu | kopensolaris*-gnu | gnu*)
2687 2684
   dynamic_linker='GNU/Linux ld.so'
2688 2685
   ;;
2689 2686
 
2690
-netbsdelf*-gnu)
2691
-  version_type=linux
2692
-  need_lib_prefix=no
2693
-  need_version=no
2694
-  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
2695
-  soname_spec='${libname}${release}${shared_ext}$major'
2696
-  shlibpath_var=LD_LIBRARY_PATH
2697
-  shlibpath_overrides_runpath=no
2698
-  hardcode_into_libs=yes
2699
-  dynamic_linker='NetBSD ld.elf_so'
2700
-  ;;
2701
-
2702 2687
 netbsd*)
2703 2688
   version_type=sunos
2704 2689
   need_lib_prefix=no
... ...
@@ -3258,6 +3243,10 @@ freebsd* | dragonfly*)
3258 3243
   fi
3259 3244
   ;;
3260 3245
 
3246
+gnu*)
3247
+  lt_cv_deplibs_check_method=pass_all
3248
+  ;;
3249
+
3261 3250
 haiku*)
3262 3251
   lt_cv_deplibs_check_method=pass_all
3263 3252
   ;;
... ...
@@ -3296,11 +3285,11 @@ irix5* | irix6* | nonstopux*)
3296 3285
   ;;
3297 3286
 
3298 3287
 # This must be glibc/ELF.
3299
-linux* | k*bsd*-gnu | kopensolaris*-gnu | gnu*)
3288
+linux* | k*bsd*-gnu | kopensolaris*-gnu)
3300 3289
   lt_cv_deplibs_check_method=pass_all
3301 3290
   ;;
3302 3291
 
3303
-netbsd* | netbsdelf*-gnu)
3292
+netbsd*)
3304 3293
   if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then
3305 3294
     lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|_pic\.a)$'
3306 3295
   else
... ...
@@ -4048,7 +4037,7 @@ m4_if([$1], [CXX], [
4048 4037
 	    ;;
4049 4038
 	esac
4050 4039
 	;;
4051
-      linux* | k*bsd*-gnu | kopensolaris*-gnu | gnu*)
4040
+      linux* | k*bsd*-gnu | kopensolaris*-gnu)
4052 4041
 	case $cc_basename in
4053 4042
 	  KCC*)
4054 4043
 	    # KAI C++ Compiler
... ...
@@ -4112,7 +4101,7 @@ m4_if([$1], [CXX], [
4112 4101
 	    ;;
4113 4102
 	esac
4114 4103
 	;;
4115
-      netbsd* | netbsdelf*-gnu)
4104
+      netbsd*)
4116 4105
 	;;
4117 4106
       *qnx* | *nto*)
4118 4107
         # QNX uses GNU C++, but need to define -shared option too, otherwise
... ...
@@ -4347,7 +4336,7 @@ m4_if([$1], [CXX], [
4347 4336
       _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
4348 4337
       ;;
4349 4338
 
4350
-    linux* | k*bsd*-gnu | kopensolaris*-gnu | gnu*)
4339
+    linux* | k*bsd*-gnu | kopensolaris*-gnu)
4351 4340
       case $cc_basename in
4352 4341
       # old Intel for x86_64 which still supported -KPIC.
4353 4342
       ecc*)
... ...
@@ -4589,9 +4578,6 @@ m4_if([$1], [CXX], [
4589 4578
       ;;
4590 4579
     esac
4591 4580
     ;;
4592
-  linux* | k*bsd*-gnu | gnu*)
4593
-    _LT_TAGVAR(link_all_deplibs, $1)=no
4594
-    ;;
4595 4581
   *)
4596 4582
     _LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
4597 4583
     ;;
... ...
@@ -4654,9 +4640,6 @@ dnl Note also adjust exclude_expsyms for C++ above.
4654 4640
   openbsd*)
4655 4641
     with_gnu_ld=no
4656 4642
     ;;
4657
-  linux* | k*bsd*-gnu | gnu*)
4658
-    _LT_TAGVAR(link_all_deplibs, $1)=no
4659
-    ;;
4660 4643
   esac
4661 4644
 
4662 4645
   _LT_TAGVAR(ld_shlibs, $1)=yes
... ...
@@ -4878,7 +4861,7 @@ _LT_EOF
4878 4861
       fi
4879 4862
       ;;
4880 4863
 
4881
-    netbsd* | netbsdelf*-gnu)
4864
+    netbsd*)
4882 4865
       if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
4883 4866
 	_LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable $libobjs $deplibs $linker_flags -o $lib'
4884 4867
 	wlarc=
... ...
@@ -5055,7 +5038,6 @@ _LT_EOF
5055 5038
 	if test "$aix_use_runtimelinking" = yes; then
5056 5039
 	  shared_flag="$shared_flag "'${wl}-G'
5057 5040
 	fi
5058
-	_LT_TAGVAR(link_all_deplibs, $1)=no
5059 5041
       else
5060 5042
 	# not using gcc
5061 5043
 	if test "$host_cpu" = ia64; then
... ...
@@ -5360,7 +5342,7 @@ _LT_EOF
5360 5342
       _LT_TAGVAR(link_all_deplibs, $1)=yes
5361 5343
       ;;
5362 5344
 
5363
-    netbsd* | netbsdelf*-gnu)
5345
+    netbsd*)
5364 5346
       if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
5365 5347
 	_LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'  # a.out
5366 5348
       else
... ...
@@ -6240,6 +6222,9 @@ if test "$_lt_caught_CXX_error" != yes; then
6240 6222
         _LT_TAGVAR(ld_shlibs, $1)=yes
6241 6223
         ;;
6242 6224
 
6225
+      gnu*)
6226
+        ;;
6227
+
6243 6228
       haiku*)
6244 6229
         _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
6245 6230
         _LT_TAGVAR(link_all_deplibs, $1)=yes
... ...
@@ -6401,7 +6386,7 @@ if test "$_lt_caught_CXX_error" != yes; then
6401 6386
         _LT_TAGVAR(inherit_rpath, $1)=yes
6402 6387
         ;;
6403 6388
 
6404
-      linux* | k*bsd*-gnu | kopensolaris*-gnu | gnu*)
6389
+      linux* | k*bsd*-gnu | kopensolaris*-gnu)
6405 6390
         case $cc_basename in
6406 6391
           KCC*)
6407 6392
 	    # Kuck and Associates, Inc. (KAI) C++ Compiler
... ...
@@ -70,7 +70,7 @@
70 70
 #         compiler:		$LTCC
71 71
 #         compiler flags:		$LTCFLAGS
72 72
 #         linker:		$LD (gnu? $with_gnu_ld)
73
-#         $progname:	(GNU libtool) 2.4.2 Debian-2.4.2-1.7ubuntu1
73
+#         $progname:	(GNU libtool) 2.4.2
74 74
 #         automake:	$automake_version
75 75
 #         autoconf:	$autoconf_version
76 76
 #
... ...
@@ -80,7 +80,7 @@
80 80
 
81 81
 PROGRAM=libtool
82 82
 PACKAGE=libtool
83
-VERSION="2.4.2 Debian-2.4.2-1.7ubuntu1"
83
+VERSION=2.4.2
84 84
 TIMESTAMP=""
85 85
 package_revision=1.3337
86 86
 
... ...
@@ -6124,10 +6124,7 @@ func_mode_link ()
6124 6124
 	case $pass in
6125 6125
 	dlopen) libs="$dlfiles" ;;
6126 6126
 	dlpreopen) libs="$dlprefiles" ;;
6127
-	link)
6128
-	  libs="$deplibs %DEPLIBS%"
6129
-	  test "X$link_all_deplibs" != Xno && libs="$libs $dependency_libs"
6130
-	  ;;
6127
+	link) libs="$deplibs %DEPLIBS% $dependency_libs" ;;
6131 6128
 	esac
6132 6129
       fi
6133 6130
       if test "$linkmode,$pass" = "lib,dlpreopen"; then
... ...
@@ -6447,19 +6444,19 @@ func_mode_link ()
6447 6444
 	    # It is a libtool convenience library, so add in its objects.
6448 6445
 	    func_append convenience " $ladir/$objdir/$old_library"
6449 6446
 	    func_append old_convenience " $ladir/$objdir/$old_library"
6450
-	    tmp_libs=
6451
-	    for deplib in $dependency_libs; do
6452
-	      deplibs="$deplib $deplibs"
6453
-	      if $opt_preserve_dup_deps ; then
6454
-		case "$tmp_libs " in
6455
-		*" $deplib "*) func_append specialdeplibs " $deplib" ;;
6456
-		esac
6457
-	      fi
6458
-	      func_append tmp_libs " $deplib"
6459
-	    done
6460 6447
 	  elif test "$linkmode" != prog && test "$linkmode" != lib; then
6461 6448
 	    func_fatal_error "\`$lib' is not a convenience library"
6462 6449
 	  fi
6450
+	  tmp_libs=
6451
+	  for deplib in $dependency_libs; do
6452
+	    deplibs="$deplib $deplibs"
6453
+	    if $opt_preserve_dup_deps ; then
6454
+	      case "$tmp_libs " in
6455
+	      *" $deplib "*) func_append specialdeplibs " $deplib" ;;
6456
+	      esac
6457
+	    fi
6458
+	    func_append tmp_libs " $deplib"
6459
+	  done
6463 6460
 	  continue
6464 6461
 	fi # $pass = conv
6465 6462
 
... ...
@@ -7352,9 +7349,6 @@ func_mode_link ()
7352 7349
 	    revision="$number_minor"
7353 7350
 	    lt_irix_increment=no
7354 7351
 	    ;;
7355
-	  *)
7356
-	    func_fatal_configuration "$modename: unknown library version type \`$version_type'"
7357
-	    ;;
7358 7352
 	  esac
7359 7353
 	  ;;
7360 7354
 	no)
... ...
@@ -1,7 +1,7 @@
1 1
 #! /bin/sh
2 2
 # Common wrapper for a few potentially missing GNU programs.
3 3
 
4
-scriptversion=2013-10-28.13; # UTC
4
+scriptversion=2012-06-26.16; # UTC
5 5
 
6 6
 # Copyright (C) 1996-2013 Free Software Foundation, Inc.
7 7
 # Originally written by Fran,cois Pinard <pinard@iro.umontreal.ca>, 1996.
... ...
@@ -160,7 +160,7 @@ give_advice ()
160 160
       ;;
161 161
    autom4te*)
162 162
       echo "You might have modified some maintainer files that require"
163
-      echo "the 'autom4te' program to be rebuilt."
163
+      echo "the 'automa4te' program to be rebuilt."
164 164
       program_details 'autom4te'
165 165
       ;;
166 166
     bison*|yacc*)
... ...
@@ -6164,8 +6164,7 @@ else
6164 6164
     ;;
6165 6165
   *)
6166 6166
     lt_cv_sys_max_cmd_len=`(getconf ARG_MAX) 2> /dev/null`
6167
-    if test -n "$lt_cv_sys_max_cmd_len" && \
6168
-	test undefined != "$lt_cv_sys_max_cmd_len"; then
6167
+    if test -n "$lt_cv_sys_max_cmd_len"; then
6169 6168
       lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4`
6170 6169
       lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3`
6171 6170
     else
... ...
@@ -6566,6 +6565,10 @@ freebsd* | dragonfly*)
6566 6565
   fi
6567 6566
   ;;
6568 6567
 
6568
+gnu*)
6569
+  lt_cv_deplibs_check_method=pass_all
6570
+  ;;
6571
+
6569 6572
 haiku*)
6570 6573
   lt_cv_deplibs_check_method=pass_all
6571 6574
   ;;
... ...
@@ -6604,11 +6607,11 @@ irix5* | irix6* | nonstopux*)
6604 6607
   ;;
6605 6608
 
6606 6609
 # This must be glibc/ELF.
6607
-linux* | k*bsd*-gnu | kopensolaris*-gnu | gnu*)
6610
+linux* | k*bsd*-gnu | kopensolaris*-gnu)
6608 6611
   lt_cv_deplibs_check_method=pass_all
6609 6612
   ;;
6610 6613
 
6611
-netbsd* | netbsdelf*-gnu)
6614
+netbsd*)
6612 6615
   if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then
6613 6616
     lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|_pic\.a)$'
6614 6617
   else
... ...
@@ -7685,7 +7688,7 @@ ia64-*-hpux*)
7685 7688
   rm -rf conftest*
7686 7689
   ;;
7687 7690
 
7688
-x86_64-*kfreebsd*-gnu|x86_64-*linux*|powerpc*-*linux*| \
7691
+x86_64-*kfreebsd*-gnu|x86_64-*linux*|ppc*-*linux*|powerpc*-*linux*| \
7689 7692
 s390*-*linux*|s390*-*tpf*|sparc*-*linux*)
7690 7693
   # Find out which ABI we are using.
7691 7694
   echo 'int i;' > conftest.$ac_ext
... ...
@@ -7701,19 +7704,9 @@ s390*-*linux*|s390*-*tpf*|sparc*-*linux*)
7701 7704
 	    LD="${LD-ld} -m elf_i386_fbsd"
7702 7705
 	    ;;
7703 7706
 	  x86_64-*linux*)
7704
-	    case `/usr/bin/file conftest.o` in
7705
-	      *x86-64*)
7706
-		LD="${LD-ld} -m elf32_x86_64"
7707
-		;;
7708
-	      *)
7709
-		LD="${LD-ld} -m elf_i386"
7710
-		;;
7711
-	    esac
7712
-	    ;;
7713
-	  powerpc64le-*)
7714
-	    LD="${LD-ld} -m elf32lppclinux"
7707
+	    LD="${LD-ld} -m elf_i386"
7715 7708
 	    ;;
7716
-	  powerpc64-*)
7709
+	  ppc64-*linux*|powerpc64-*linux*)
7717 7710
 	    LD="${LD-ld} -m elf32ppclinux"
7718 7711
 	    ;;
7719 7712
 	  s390x-*linux*)
... ...
@@ -7732,10 +7725,7 @@ s390*-*linux*|s390*-*tpf*|sparc*-*linux*)
7732 7725
 	  x86_64-*linux*)
7733 7726
 	    LD="${LD-ld} -m elf_x86_64"
7734 7727
 	    ;;
7735
-	  powerpcle-*)
7736
-	    LD="${LD-ld} -m elf64lppc"
7737
-	    ;;
7738
-	  powerpc-*)
7728
+	  ppc*-*linux*|powerpc*-*linux*)
7739 7729
 	    LD="${LD-ld} -m elf64ppc"
7740 7730
 	    ;;
7741 7731
 	  s390*-*linux*|s390*-*tpf*)
... ...
@@ -9543,7 +9533,7 @@ lt_prog_compiler_static=
9543 9533
       lt_prog_compiler_static='-non_shared'
9544 9534
       ;;
9545 9535
 
9546
-    linux* | k*bsd*-gnu | kopensolaris*-gnu | gnu*)
9536
+    linux* | k*bsd*-gnu | kopensolaris*-gnu)
9547 9537
       case $cc_basename in
9548 9538
       # old Intel for x86_64 which still supported -KPIC.
9549 9539
       ecc*)
... ...
@@ -10021,9 +10011,6 @@ $as_echo_n "checking whether the $compiler linker ($LD) supports shared librarie
10021 10011
   openbsd*)
10022 10012
     with_gnu_ld=no
10023 10013
     ;;
10024
-  linux* | k*bsd*-gnu | gnu*)
10025
-    link_all_deplibs=no
10026
-    ;;
10027 10014
   esac
10028 10015
 
10029 10016
   ld_shlibs=yes
... ...
@@ -10245,7 +10232,7 @@ _LT_EOF
10245 10232
       fi
10246 10233
       ;;
10247 10234
 
10248
-    netbsd* | netbsdelf*-gnu)
10235
+    netbsd*)
10249 10236
       if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
10250 10237
 	archive_cmds='$LD -Bshareable $libobjs $deplibs $linker_flags -o $lib'
10251 10238
 	wlarc=
... ...
@@ -10422,7 +10409,6 @@ _LT_EOF
10422 10409
 	if test "$aix_use_runtimelinking" = yes; then
10423 10410
 	  shared_flag="$shared_flag "'${wl}-G'
10424 10411
 	fi
10425
-	link_all_deplibs=no
10426 10412
       else
10427 10413
 	# not using gcc
10428 10414
 	if test "$host_cpu" = ia64; then
... ...
@@ -10876,7 +10862,7 @@ $as_echo "$lt_cv_irix_exported_symbol" >&6; }
10876 10862
       link_all_deplibs=yes
10877 10863
       ;;
10878 10864
 
10879
-    netbsd* | netbsdelf*-gnu)
10865
+    netbsd*)
10880 10866
       if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
10881 10867
 	archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'  # a.out
10882 10868
       else
... ...
@@ -11713,6 +11699,17 @@ freebsd* | dragonfly*)
11713 11699
   esac
11714 11700
   ;;
11715 11701
 
11702
+gnu*)
11703
+  version_type=linux # correct to gnu/linux during the next big refactor
11704
+  need_lib_prefix=no
11705
+  need_version=no
11706
+  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}'
11707
+  soname_spec='${libname}${release}${shared_ext}$major'
11708
+  shlibpath_var=LD_LIBRARY_PATH
11709
+  shlibpath_overrides_runpath=no
11710
+  hardcode_into_libs=yes
11711
+  ;;
11712
+
11716 11713
 haiku*)
11717 11714
   version_type=linux # correct to gnu/linux during the next big refactor
11718 11715
   need_lib_prefix=no
... ...
@@ -11829,7 +11826,7 @@ linux*oldld* | linux*aout* | linux*coff*)
11829 11826
   ;;
11830 11827
 
11831 11828
 # This must be glibc/ELF.
11832
-linux* | k*bsd*-gnu | kopensolaris*-gnu | gnu*)
11829
+linux* | k*bsd*-gnu | kopensolaris*-gnu)
11833 11830
   version_type=linux # correct to gnu/linux during the next big refactor
11834 11831
   need_lib_prefix=no
11835 11832
   need_version=no
... ...
@@ -11893,18 +11890,6 @@ fi
11893 11890
   dynamic_linker='GNU/Linux ld.so'
11894 11891
   ;;
11895 11892
 
11896
-netbsdelf*-gnu)
11897
-  version_type=linux
11898
-  need_lib_prefix=no
11899
-  need_version=no
11900
-  library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
11901
-  soname_spec='${libname}${release}${shared_ext}$major'
11902
-  shlibpath_var=LD_LIBRARY_PATH
11903
-  shlibpath_overrides_runpath=no
11904
-  hardcode_into_libs=yes
11905
-  dynamic_linker='NetBSD ld.elf_so'
11906
-  ;;
11907
-
11908 11893
 netbsd*)
11909 11894
   version_type=sunos
11910 11895
   need_lib_prefix=no
... ...
@@ -1,4 +1,4 @@
1
-static char rcsid[] = "$Id: bamread.c 160725 2015-03-11 16:45:17Z twu $";
1
+static char rcsid[] = "$Id: bamread.c 163197 2015-04-13 21:57:42Z twu $";
2 2
 #ifdef HAVE_CONFIG_H
3 3
 #include <config.h>
4 4
 #endif
... ...
@@ -1891,10 +1891,16 @@ Bamline_new (char *acc, unsigned int flag, int nhits, bool good_unique_p, int ma
1891 1891
 
1892 1892
   if (copy_aux_contents_p == true) {
1893 1893
     new->aux_length = aux_end - aux_start;
1894
-    new->aux_contents = (uint8_t *) MALLOC(new->aux_length * sizeof(unsigned char));
1895
-    memcpy(new->aux_contents,aux_start,new->aux_length);
1896
-    new->aux_start = (unsigned char *) new->aux_contents;
1897
-    new->aux_end = new->aux_start + new->aux_length;
1894
+    if (new->aux_length == 0) {
1895
+      new->aux_contents = (uint8_t *) NULL;
1896
+      new->aux_start = (uint8_t *) NULL;
1897
+      new->aux_end = (uint8_t *) NULL;
1898
+    } else {
1899
+      new->aux_contents = (uint8_t *) MALLOC(new->aux_length * sizeof(unsigned char));
1900
+      memcpy(new->aux_contents,aux_start,new->aux_length);
1901
+      new->aux_start = (unsigned char *) new->aux_contents;
1902
+      new->aux_end = new->aux_start + new->aux_length;
1903
+    }
1898 1904
   } else {
1899 1905
     /* Point to bam->data */
1900 1906
     new->aux_contents = (uint8_t *) NULL;
... ...
@@ -1,5 +1,4 @@
1
-#define DEBUG2 1
2
-static char rcsid[] = "$Id: bamtally.c 161991 2015-03-25 23:24:46Z twu $";
1
+static char rcsid[] = "$Id: bamtally.c 172388 2015-08-21 20:10:50Z twu $";
3 2
 #ifdef HAVE_CONFIG_H
4 3
 #include <config.h>
5 4
 #endif
... ...
@@ -1584,7 +1583,7 @@ static Ucharlist_T
1584 1583
 push_string (int *nbytes, Ucharlist_T list, char *string) {
1585 1584
   int length, i;
1586 1585
 
1587
-  debug2(printf("%d: Pushing char %s\n",*nbytes,string));
1586
+  debug2(printf("%d: Pushing string %s\n",*nbytes,string));
1588 1587
   length = strlen(string);
1589 1588
   for (i = 0; i < length; i++) {
1590 1589
     list = Ucharlist_push(list,string[i]);
... ...
@@ -2287,7 +2286,7 @@ process_codons_plus (Ucharlist_T bytes, int *nbytes, Tally_T tally0, Tally_T tal
2287 2286
 
2288 2287
 	    Codon_free(&(array[i]));
2289 2288
 	  }
2290
-
2289
+	  
2291 2290
 	  FREE(array);
2292 2291
 	  List_free(&alt_codons);
2293 2292
 	}
... ...
@@ -2330,10 +2329,10 @@ process_codons_plus (Ucharlist_T bytes, int *nbytes, Tally_T tally0, Tally_T tal
2330 2329
 	    }
2331 2330
 	    Codon_free(&(array[i]));
2332 2331
 	  }
2333
-	}
2334 2332
 
2335
-	FREE(array);
2336
-	List_free(&alt_codons);
2333
+	  FREE(array);
2334
+	  List_free(&alt_codons);
2335
+	}
2337 2336
       }
2338 2337
     }
2339 2338
   }
... ...
@@ -2577,10 +2576,10 @@ process_codons_minus (Ucharlist_T bytes, int *nbytes, Tally_T tally0, Tally_T ta
2577 2576
 	    }
2578 2577
 	    Codon_free(&(array[i]));
2579 2578
 	  }
2580
-	}
2581 2579
 
2582
-	FREE(array);
2583
-	List_free(&alt_codons);
2580
+	  FREE(array);
2581
+	  List_free(&alt_codons);
2582
+	}
2584 2583
       }
2585 2584
     }
2586 2585
   }
... ...
@@ -4366,10 +4365,13 @@ iit_block (List_T *intervallist, List_T *labellist, List_T *datalist,
4366 4365
 	for (i = 0; i < ndeletions; i++) {
4367 4366
 	  del0 = del_array_byshift[i];
4368 4367
 	  /* Counts and segment for deletion i */
4368
+	  debug2(printf("plus and minus counts for deletion\n"));
4369 4369
 	  bytes = push_int(&nbytes,bytes,del0->count_plus);
4370 4370
 	  bytes = push_int(&nbytes,bytes,del0->count_minus);
4371
+	  debug2(printf("plus and minus counts for reference\n"));
4371 4372
 	  bytes = push_int(&nbytes,bytes,this->n_fromleft_plus); /* ref count */
4372 4373
 	  bytes = push_int(&nbytes,bytes,this->n_fromleft_minus); /* ref count */
4374
+	  debug2(printf("Deletion string:\n"));
4373 4375
 	  bytes = push_string(&nbytes,bytes,del0->segment);
4374 4376
 
4375 4377
 	  /* Cycles for deletion i */
... ...
@@ -5766,12 +5768,11 @@ best_mapping_p (Tableuint_T resolve_low_table, Tableuint_T resolve_high_table, c
5766 5768
 
5767 5769
 
5768 5770
 static void
5769
-get_passing_counts (__m128i *counts, int readlength, Bamline_T *bamlines, int nreps, int minimum_quality_score) {
5771
+get_passing_counts (__m128i *counts, int ncounts, int readlength, Bamline_T *bamlines, int nreps, int minimum_quality_score) {
5770 5772
   int i, r, b;
5771 5773
   char *quality_string, buffer[16];
5772 5774
   int x;
5773 5775
 
5774
-
5775 5776
   __m128i block, cmp16, cmp8, threshold, ones;
5776 5777
   __m128i foo;
5777 5778
 
... ...
@@ -5792,23 +5793,35 @@ get_passing_counts (__m128i *counts, int readlength, Bamline_T *bamlines, int nr
5792 5793
       counts[b] = _mm_set1_epi16(0);
5793 5794
     }
5794 5795
   }
5796
+  if (b > ncounts) {
5797
+    fprintf(stderr,"Allocated only %d vectors, but need %d\n",ncounts,b);
5798
+    abort();
5799
+  }
5795 5800
 
5796 5801
   for (i = 0; i < nreps; i++) {
5797 5802
     quality_string = Bamline_quality_string(bamlines[0]);
5798 5803
     /* printf("quality string: %s\n",quality_string); */
5799 5804
     b = 0; r = 0;
5800 5805
     while (r + 16 < readlength) {
5801
-      block = _mm_loadu_si128((__m128i *) &(quality_string[r]));
5806
+      block = _mm_loadu_si128((__m128i *) &(quality_string[r])); /* Put 16 bytes of quality string into block */
5807
+
5808
+      /* Count bytes where (threshold > quality).  "true": 0xFF => 0.
5809
+	 "false": 0x00 => 1.  Equivalently, cmp8 contains a 1 whenever
5810
+	 quality >= threshold. */
5802 5811
       cmp8 = _mm_add_epi8(_mm_cmpgt_epi8(threshold,block),ones);
5812
+
5813
+      /* Tally the lower 8 bytes */
5803 5814
       cmp16 = _mm_cvtepi8_epi16(cmp8);
5804 5815
       counts[b] = _mm_add_epi16(counts[b],cmp16); b++;
5805 5816
 
5817
+      /* Tally the upper 8 bytes */
5806 5818
       cmp16 = _mm_cvtepi8_epi16(_mm_srli_si128(cmp8,8));
5807 5819
       counts[b] = _mm_add_epi16(counts[b],cmp16); b++;
5808 5820
 
5809 5821
       r += 16;
5810 5822
     }
5811 5823
     if (r < readlength) {
5824
+      /* Handle the last 8 bytes */
5812 5825
       strncpy(buffer,&(quality_string[r]),readlength-r);
5813 5826
       block = _mm_loadu_si128((__m128i *) buffer);
5814 5827
       cmp8 = _mm_add_epi8(_mm_cmpgt_epi8(threshold,block),ones);
... ...
@@ -5898,7 +5911,8 @@ Bamtally_run (long int **tally_matches, long int **tally_mismatches,
5898 5911
   unsigned int linei = 0, linei_start, linei_end;
5899 5912
   int nlines;
5900 5913
   int nreps;
5901
-  __m128i counts[50], foo;
5914
+  __m128i *counts, foo;
5915
+  int ncounts;
5902 5916
   int i;
5903 5917
 
5904 5918
 
... ...
@@ -6013,13 +6027,16 @@ Bamtally_run (long int **tally_matches, long int **tally_mismatches,
6013 6027
 			genome,chroffset,ignore_query_Ns_p,print_indels_p,readlevel_p,
6014 6028
 			max_softclip,linei+linei_start,/*counts*/NULL,nreps);
6015 6029
 	  } else {
6016
-	    get_passing_counts(counts,readlength,&(bamlines[linei_start]),nreps,minimum_quality_score);
6030
+	    ncounts = (readlength + 7)/8;
6031
+	    counts = (__m128i *) _mm_malloc(ncounts * sizeof(__m128i),16);
6032
+	    get_passing_counts(counts,ncounts,readlength,&(bamlines[linei_start]),nreps,minimum_quality_score);
6017 6033
 	    revise_read(alloc_tallies,chrstart,chrend,chrpos_low,Bamline_flag(bamline_rep),
6018 6034
 			Bamline_cigar_types(bamline_rep),Bamline_cigar_npositions(bamline_rep),
6019 6035
 			Bamline_cigar_querylength(bamline_rep),rsequence,Bamline_nm(bamline_rep),
6020 6036
 			Bamline_splice_strand(bamline_rep),Bamline_terminalp(bamline_rep),alloc_low,
6021 6037
 			genome,chroffset,ignore_query_Ns_p,print_indels_p,readlevel_p,
6022 6038
 			max_softclip,linei+linei_start,counts,nreps);
6039
+	    _mm_free(counts);
6023 6040
 	  }
6024 6041
 	  goodp = true;
6025 6042
 	}
... ...
@@ -6167,7 +6184,9 @@ Bamtally_run (long int **tally_matches, long int **tally_mismatches,
6167 6184
 			max_softclip,linei + linei_start,/*counts*/NULL,nreps);
6168 6185
 	  } else {
6169 6186
 	    readlength = Bamline_readlength(bamline_rep);
6170
-	    get_passing_counts(counts,readlength,&(bamlines[linei_start]),nreps,minimum_quality_score);
6187
+	    ncounts = (readlength + 7)/8;
6188
+	    counts = (__m128i *) _mm_malloc(ncounts * sizeof(__m128i),16);
6189
+	    get_passing_counts(counts,ncounts,readlength,&(bamlines[linei_start]),nreps,minimum_quality_score);
6171 6190
 	    revise_read(alloc_tallies,chrstart,chrend,chrpos_low,Bamline_flag(bamline_rep),
6172 6191
 			Bamline_cigar_types(bamline_rep),Bamline_cigar_npositions(bamline_rep),
6173 6192
 			Bamline_cigar_querylength(bamline_rep),Bamline_read(bamline_rep),