[med-svn] [Git][med-team/biobambam2][master] 4 commits: New upstream version 2.0.152+dfsg
Steffen Möller
gitlab at salsa.debian.org
Fri Jan 24 13:39:30 GMT 2020
Steffen Möller pushed to branch master at Debian Med / biobambam2
Commits:
fcb2ab68 by Steffen Moeller at 2020-01-24T12:36:54+01:00
New upstream version 2.0.152+dfsg
- - - - -
771ff5c9 by Steffen Moeller at 2020-01-24T12:36:54+01:00
routine-update: New upstream version
- - - - -
104a403d by Steffen Moeller at 2020-01-24T12:36:55+01:00
Update upstream source from tag 'upstream/2.0.152+dfsg'
Update to upstream version '2.0.152+dfsg'
with Debian dir 1afe92acaddcf0072e4f2c1f0bbf1384e8d5cfa9
- - - - -
6ebd913d by Steffen Moeller at 2020-01-24T13:17:24+01:00
routine-update: Ready to upload to unstable
- - - - -
15 changed files:
- .gitignore
- ChangeLog
- config.guess
- config.sub
- configure.ac
- debian/changelog
- debian/control
- src/Makefile.am
- src/programs/bamauxmerge2.cpp
- src/programs/bamconsensus.cpp
- src/programs/bamfeaturecount.cpp
- src/programs/bamfilterk.cpp
- src/programs/bamtofastq.1
- src/programs/bamtofastq.cpp
- + src/programs/vcfreplacecontigs.cpp
Changes:
=====================================
.gitignore
=====================================
@@ -64,4 +64,5 @@ src/populaterefcache
src/vcfconcat
src/vcfsort
removespace.sh
-src/filtergtf
\ No newline at end of file
+src/filtergtf
+src/vcfreplacecontigs
=====================================
ChangeLog
=====================================
@@ -1,3 +1,35 @@
+biobambam2 (2.0.152-1) unstable; urgency=medium
+
+ * update libmaus2 version to 2.0.694
+
+ -- German Tischler-Höhle <germant at miltenyibiotec.de> Wed, 22 Jan 2020 09:58:27 +0100
+
+biobambam2 (2.0.151-1) unstable; urgency=medium
+
+ * bump libmaus2 version
+
+ -- German Tischler-Höhle <germant at miltenyibiotec.de> Tue, 21 Jan 2020 16:41:38 +0100
+
+biobambam2 (2.0.150-1) unstable; urgency=medium
+
+ * Add cols (line wrapping) option in bamtofastq
+
+ -- German Tischler-Höhle <germant at miltenyibiotec.de> Tue, 07 Jan 2020 16:37:02 +0100
+
+biobambam2 (2.0.149-1) unstable; urgency=medium
+
+ * use kmerCallbackPosFR instead of kmerCallbackPos in bamfilterk
+ * Add vcfreplacecontigs program
+
+ -- German Tischler-Höhle <germant at miltenyibiotec.de> Tue, 07 Jan 2020 09:02:29 +0100
+
+biobambam2 (2.0.148-1) unstable; urgency=medium
+
+ * compute maximum depth in bamfeaturecount
+ * fix output of wrong reference id in bamfeaturecount if GTF chrom set is a subset of BAM chrom set
+
+ -- German Tischler-Höhle <germant at miltenyibiotec.de> Wed, 13 Nov 2019 12:53:00 +0100
+
biobambam2 (2.0.147-1) unstable; urgency=medium
* fix heap comparisons in bamconsensus
=====================================
config.guess
=====================================
@@ -1,8 +1,8 @@
#! /bin/sh
# Attempt to guess a canonical system name.
-# Copyright 1992-2015 Free Software Foundation, Inc.
+# Copyright 1992-2018 Free Software Foundation, Inc.
-timestamp='2015-08-20'
+timestamp='2018-02-24'
# This file is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
@@ -15,7 +15,7 @@ timestamp='2015-08-20'
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
-# along with this program; if not, see <http://www.gnu.org/licenses/>.
+# along with this program; if not, see <https://www.gnu.org/licenses/>.
#
# As a special exception to the GNU General Public License, if you
# distribute this file as part of a program that contains a
@@ -27,7 +27,7 @@ timestamp='2015-08-20'
# Originally written by Per Bothner; maintained since 2000 by Ben Elliston.
#
# You can get the latest version of this script from:
-# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD
+# https://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess
#
# Please send patches to <config-patches at gnu.org>.
@@ -39,7 +39,7 @@ Usage: $0 [OPTION]
Output the configuration name of the system \`$me' is run on.
-Operation modes:
+Options:
-h, --help print this help, then exit
-t, --time-stamp print date of last modification, then exit
-v, --version print version number, then exit
@@ -50,7 +50,7 @@ version="\
GNU config.guess ($timestamp)
Originally written by Per Bothner.
-Copyright 1992-2015 Free Software Foundation, Inc.
+Copyright 1992-2018 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
@@ -107,9 +107,9 @@ trap "rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null; exit 1" 1 2 13 15 ;
dummy=$tmp/dummy ;
tmpfiles="$dummy.c $dummy.o $dummy.rel $dummy" ;
case $CC_FOR_BUILD,$HOST_CC,$CC in
- ,,) echo "int x;" > $dummy.c ;
+ ,,) echo "int x;" > "$dummy.c" ;
for c in cc gcc c89 c99 ; do
- if ($c -c -o $dummy.o $dummy.c) >/dev/null 2>&1 ; then
+ if ($c -c -o "$dummy.o" "$dummy.c") >/dev/null 2>&1 ; then
CC_FOR_BUILD="$c"; break ;
fi ;
done ;
@@ -132,14 +132,14 @@ UNAME_RELEASE=`(uname -r) 2>/dev/null` || UNAME_RELEASE=unknown
UNAME_SYSTEM=`(uname -s) 2>/dev/null` || UNAME_SYSTEM=unknown
UNAME_VERSION=`(uname -v) 2>/dev/null` || UNAME_VERSION=unknown
-case "${UNAME_SYSTEM}" in
+case "$UNAME_SYSTEM" in
Linux|GNU|GNU/*)
# If the system lacks a compiler, then just pick glibc.
# We could probably try harder.
LIBC=gnu
- eval $set_cc_for_build
- cat <<-EOF > $dummy.c
+ eval "$set_cc_for_build"
+ cat <<-EOF > "$dummy.c"
#include <features.h>
#if defined(__UCLIBC__)
LIBC=uclibc
@@ -149,13 +149,20 @@ Linux|GNU|GNU/*)
LIBC=gnu
#endif
EOF
- eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^LIBC' | sed 's, ,,g'`
+ eval "`$CC_FOR_BUILD -E "$dummy.c" 2>/dev/null | grep '^LIBC' | sed 's, ,,g'`"
+
+ # If ldd exists, use it to detect musl libc.
+ if command -v ldd >/dev/null && \
+ ldd --version 2>&1 | grep -q ^musl
+ then
+ LIBC=musl
+ fi
;;
esac
# Note: order is significant - the case branches are not exclusive.
-case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
+case "$UNAME_MACHINE:$UNAME_SYSTEM:$UNAME_RELEASE:$UNAME_VERSION" in
*:NetBSD:*:*)
# NetBSD (nbsd) targets should (where applicable) match one or
# more of the tuples: *-*-netbsdelf*, *-*-netbsdaout*,
@@ -169,27 +176,30 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
# portion of the name. We always set it to "unknown".
sysctl="sysctl -n hw.machine_arch"
UNAME_MACHINE_ARCH=`(uname -p 2>/dev/null || \
- /sbin/$sysctl 2>/dev/null || \
- /usr/sbin/$sysctl 2>/dev/null || \
+ "/sbin/$sysctl" 2>/dev/null || \
+ "/usr/sbin/$sysctl" 2>/dev/null || \
echo unknown)`
- case "${UNAME_MACHINE_ARCH}" in
+ case "$UNAME_MACHINE_ARCH" in
armeb) machine=armeb-unknown ;;
arm*) machine=arm-unknown ;;
sh3el) machine=shl-unknown ;;
sh3eb) machine=sh-unknown ;;
sh5el) machine=sh5le-unknown ;;
earmv*)
- arch=`echo ${UNAME_MACHINE_ARCH} | sed -e 's,^e\(armv[0-9]\).*$,\1,'`
- endian=`echo ${UNAME_MACHINE_ARCH} | sed -ne 's,^.*\(eb\)$,\1,p'`
- machine=${arch}${endian}-unknown
+ arch=`echo "$UNAME_MACHINE_ARCH" | sed -e 's,^e\(armv[0-9]\).*$,\1,'`
+ endian=`echo "$UNAME_MACHINE_ARCH" | sed -ne 's,^.*\(eb\)$,\1,p'`
+ machine="${arch}${endian}"-unknown
;;
- *) machine=${UNAME_MACHINE_ARCH}-unknown ;;
+ *) machine="$UNAME_MACHINE_ARCH"-unknown ;;
esac
# The Operating System including object format, if it has switched
- # to ELF recently, or will in the future.
- case "${UNAME_MACHINE_ARCH}" in
- arm*|earm*|i386|m68k|ns32k|sh3*|sparc|vax)
- eval $set_cc_for_build
+ # to ELF recently (or will in the future) and ABI.
+ case "$UNAME_MACHINE_ARCH" in
+ earm*)
+ os=netbsdelf
+ ;;
+ arm*|i386|m68k|ns32k|sh3*|sparc|vax)
+ eval "$set_cc_for_build"
if echo __ELF__ | $CC_FOR_BUILD -E - 2>/dev/null \
| grep -q __ELF__
then
@@ -205,10 +215,10 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
;;
esac
# Determine ABI tags.
- case "${UNAME_MACHINE_ARCH}" in
+ case "$UNAME_MACHINE_ARCH" in
earm*)
expr='s/^earmv[0-9]/-eabi/;s/eb$//'
- abi=`echo ${UNAME_MACHINE_ARCH} | sed -e "$expr"`
+ abi=`echo "$UNAME_MACHINE_ARCH" | sed -e "$expr"`
;;
esac
# The OS release
@@ -216,42 +226,55 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
# thus, need a distinct triplet. However, they do not need
# kernel version information, so it can be replaced with a
# suitable tag, in the style of linux-gnu.
- case "${UNAME_VERSION}" in
+ case "$UNAME_VERSION" in
Debian*)
release='-gnu'
;;
*)
- release=`echo ${UNAME_RELEASE} | sed -e 's/[-_].*//' | cut -d. -f1,2`
+ release=`echo "$UNAME_RELEASE" | sed -e 's/[-_].*//' | cut -d. -f1,2`
;;
esac
# Since CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM:
# contains redundant information, the shorter form:
# CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM is used.
- echo "${machine}-${os}${release}${abi}"
+ echo "$machine-${os}${release}${abi}"
exit ;;
*:Bitrig:*:*)
UNAME_MACHINE_ARCH=`arch | sed 's/Bitrig.//'`
- echo ${UNAME_MACHINE_ARCH}-unknown-bitrig${UNAME_RELEASE}
+ echo "$UNAME_MACHINE_ARCH"-unknown-bitrig"$UNAME_RELEASE"
exit ;;
*:OpenBSD:*:*)
UNAME_MACHINE_ARCH=`arch | sed 's/OpenBSD.//'`
- echo ${UNAME_MACHINE_ARCH}-unknown-openbsd${UNAME_RELEASE}
+ echo "$UNAME_MACHINE_ARCH"-unknown-openbsd"$UNAME_RELEASE"
+ exit ;;
+ *:LibertyBSD:*:*)
+ UNAME_MACHINE_ARCH=`arch | sed 's/^.*BSD\.//'`
+ echo "$UNAME_MACHINE_ARCH"-unknown-libertybsd"$UNAME_RELEASE"
+ exit ;;
+ *:MidnightBSD:*:*)
+ echo "$UNAME_MACHINE"-unknown-midnightbsd"$UNAME_RELEASE"
exit ;;
*:ekkoBSD:*:*)
- echo ${UNAME_MACHINE}-unknown-ekkobsd${UNAME_RELEASE}
+ echo "$UNAME_MACHINE"-unknown-ekkobsd"$UNAME_RELEASE"
exit ;;
*:SolidBSD:*:*)
- echo ${UNAME_MACHINE}-unknown-solidbsd${UNAME_RELEASE}
+ echo "$UNAME_MACHINE"-unknown-solidbsd"$UNAME_RELEASE"
exit ;;
macppc:MirBSD:*:*)
- echo powerpc-unknown-mirbsd${UNAME_RELEASE}
+ echo powerpc-unknown-mirbsd"$UNAME_RELEASE"
exit ;;
*:MirBSD:*:*)
- echo ${UNAME_MACHINE}-unknown-mirbsd${UNAME_RELEASE}
+ echo "$UNAME_MACHINE"-unknown-mirbsd"$UNAME_RELEASE"
exit ;;
*:Sortix:*:*)
- echo ${UNAME_MACHINE}-unknown-sortix
+ echo "$UNAME_MACHINE"-unknown-sortix
exit ;;
+ *:Redox:*:*)
+ echo "$UNAME_MACHINE"-unknown-redox
+ exit ;;
+ mips:OSF1:*.*)
+ echo mips-dec-osf1
+ exit ;;
alpha:OSF1:*:*)
case $UNAME_RELEASE in
*4.0)
@@ -268,63 +291,54 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
ALPHA_CPU_TYPE=`/usr/sbin/psrinfo -v | sed -n -e 's/^ The alpha \(.*\) processor.*$/\1/p' | head -n 1`
case "$ALPHA_CPU_TYPE" in
"EV4 (21064)")
- UNAME_MACHINE="alpha" ;;
+ UNAME_MACHINE=alpha ;;
"EV4.5 (21064)")
- UNAME_MACHINE="alpha" ;;
+ UNAME_MACHINE=alpha ;;
"LCA4 (21066/21068)")
- UNAME_MACHINE="alpha" ;;
+ UNAME_MACHINE=alpha ;;
"EV5 (21164)")
- UNAME_MACHINE="alphaev5" ;;
+ UNAME_MACHINE=alphaev5 ;;
"EV5.6 (21164A)")
- UNAME_MACHINE="alphaev56" ;;
+ UNAME_MACHINE=alphaev56 ;;
"EV5.6 (21164PC)")
- UNAME_MACHINE="alphapca56" ;;
+ UNAME_MACHINE=alphapca56 ;;
"EV5.7 (21164PC)")
- UNAME_MACHINE="alphapca57" ;;
+ UNAME_MACHINE=alphapca57 ;;
"EV6 (21264)")
- UNAME_MACHINE="alphaev6" ;;
+ UNAME_MACHINE=alphaev6 ;;
"EV6.7 (21264A)")
- UNAME_MACHINE="alphaev67" ;;
+ UNAME_MACHINE=alphaev67 ;;
"EV6.8CB (21264C)")
- UNAME_MACHINE="alphaev68" ;;
+ UNAME_MACHINE=alphaev68 ;;
"EV6.8AL (21264B)")
- UNAME_MACHINE="alphaev68" ;;
+ UNAME_MACHINE=alphaev68 ;;
"EV6.8CX (21264D)")
- UNAME_MACHINE="alphaev68" ;;
+ UNAME_MACHINE=alphaev68 ;;
"EV6.9A (21264/EV69A)")
- UNAME_MACHINE="alphaev69" ;;
+ UNAME_MACHINE=alphaev69 ;;
"EV7 (21364)")
- UNAME_MACHINE="alphaev7" ;;
+ UNAME_MACHINE=alphaev7 ;;
"EV7.9 (21364A)")
- UNAME_MACHINE="alphaev79" ;;
+ UNAME_MACHINE=alphaev79 ;;
esac
# A Pn.n version is a patched version.
# A Vn.n version is a released version.
# A Tn.n version is a released field test version.
# A Xn.n version is an unreleased experimental baselevel.
# 1.2 uses "1.2" for uname -r.
- echo ${UNAME_MACHINE}-dec-osf`echo ${UNAME_RELEASE} | sed -e 's/^[PVTX]//' | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'`
+ echo "$UNAME_MACHINE"-dec-osf"`echo "$UNAME_RELEASE" | sed -e 's/^[PVTX]//' | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz`"
# Reset EXIT trap before exiting to avoid spurious non-zero exit code.
exitcode=$?
trap '' 0
exit $exitcode ;;
- Alpha\ *:Windows_NT*:*)
- # How do we know it's Interix rather than the generic POSIX subsystem?
- # Should we change UNAME_MACHINE based on the output of uname instead
- # of the specific Alpha model?
- echo alpha-pc-interix
- exit ;;
- 21064:Windows_NT:50:3)
- echo alpha-dec-winnt3.5
- exit ;;
Amiga*:UNIX_System_V:4.0:*)
echo m68k-unknown-sysv4
exit ;;
*:[Aa]miga[Oo][Ss]:*:*)
- echo ${UNAME_MACHINE}-unknown-amigaos
+ echo "$UNAME_MACHINE"-unknown-amigaos
exit ;;
*:[Mm]orph[Oo][Ss]:*:*)
- echo ${UNAME_MACHINE}-unknown-morphos
+ echo "$UNAME_MACHINE"-unknown-morphos
exit ;;
*:OS/390:*:*)
echo i370-ibm-openedition
@@ -336,7 +350,7 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
echo powerpc-ibm-os400
exit ;;
arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*)
- echo arm-acorn-riscix${UNAME_RELEASE}
+ echo arm-acorn-riscix"$UNAME_RELEASE"
exit ;;
arm*:riscos:*:*|arm*:RISCOS:*:*)
echo arm-unknown-riscos
@@ -363,38 +377,38 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
sparc) echo sparc-icl-nx7; exit ;;
esac ;;
s390x:SunOS:*:*)
- echo ${UNAME_MACHINE}-ibm-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ echo "$UNAME_MACHINE"-ibm-solaris2"`echo "$UNAME_RELEASE" | sed -e 's/[^.]*//'`"
exit ;;
sun4H:SunOS:5.*:*)
- echo sparc-hal-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ echo sparc-hal-solaris2"`echo "$UNAME_RELEASE"|sed -e 's/[^.]*//'`"
exit ;;
sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*)
- echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ echo sparc-sun-solaris2"`echo "$UNAME_RELEASE" | sed -e 's/[^.]*//'`"
exit ;;
i86pc:AuroraUX:5.*:* | i86xen:AuroraUX:5.*:*)
- echo i386-pc-auroraux${UNAME_RELEASE}
+ echo i386-pc-auroraux"$UNAME_RELEASE"
exit ;;
i86pc:SunOS:5.*:* | i86xen:SunOS:5.*:*)
- eval $set_cc_for_build
- SUN_ARCH="i386"
+ eval "$set_cc_for_build"
+ SUN_ARCH=i386
# If there is a compiler, see if it is configured for 64-bit objects.
# Note that the Sun cc does not turn __LP64__ into 1 like gcc does.
# This test works for both compilers.
- if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then
+ if [ "$CC_FOR_BUILD" != no_compiler_found ]; then
if (echo '#ifdef __amd64'; echo IS_64BIT_ARCH; echo '#endif') | \
- (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \
+ (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \
grep IS_64BIT_ARCH >/dev/null
then
- SUN_ARCH="x86_64"
+ SUN_ARCH=x86_64
fi
fi
- echo ${SUN_ARCH}-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ echo "$SUN_ARCH"-pc-solaris2"`echo "$UNAME_RELEASE"|sed -e 's/[^.]*//'`"
exit ;;
sun4*:SunOS:6*:*)
# According to config.sub, this is the proper way to canonicalize
# SunOS6. Hard to guess exactly what SunOS6 will be like, but
# it's likely to be more like Solaris than SunOS4.
- echo sparc-sun-solaris3`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ echo sparc-sun-solaris3"`echo "$UNAME_RELEASE"|sed -e 's/[^.]*//'`"
exit ;;
sun4*:SunOS:*:*)
case "`/usr/bin/arch -k`" in
@@ -403,25 +417,25 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
;;
esac
# Japanese Language versions have a version number like `4.1.3-JL'.
- echo sparc-sun-sunos`echo ${UNAME_RELEASE}|sed -e 's/-/_/'`
+ echo sparc-sun-sunos"`echo "$UNAME_RELEASE"|sed -e 's/-/_/'`"
exit ;;
sun3*:SunOS:*:*)
- echo m68k-sun-sunos${UNAME_RELEASE}
+ echo m68k-sun-sunos"$UNAME_RELEASE"
exit ;;
sun*:*:4.2BSD:*)
UNAME_RELEASE=`(sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null`
- test "x${UNAME_RELEASE}" = "x" && UNAME_RELEASE=3
+ test "x$UNAME_RELEASE" = x && UNAME_RELEASE=3
case "`/bin/arch`" in
sun3)
- echo m68k-sun-sunos${UNAME_RELEASE}
+ echo m68k-sun-sunos"$UNAME_RELEASE"
;;
sun4)
- echo sparc-sun-sunos${UNAME_RELEASE}
+ echo sparc-sun-sunos"$UNAME_RELEASE"
;;
esac
exit ;;
aushp:SunOS:*:*)
- echo sparc-auspex-sunos${UNAME_RELEASE}
+ echo sparc-auspex-sunos"$UNAME_RELEASE"
exit ;;
# The situation for MiNT is a little confusing. The machine name
# can be virtually everything (everything which is not
@@ -432,44 +446,44 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
# MiNT. But MiNT is downward compatible to TOS, so this should
# be no problem.
atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*)
- echo m68k-atari-mint${UNAME_RELEASE}
+ echo m68k-atari-mint"$UNAME_RELEASE"
exit ;;
atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*)
- echo m68k-atari-mint${UNAME_RELEASE}
+ echo m68k-atari-mint"$UNAME_RELEASE"
exit ;;
*falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*)
- echo m68k-atari-mint${UNAME_RELEASE}
+ echo m68k-atari-mint"$UNAME_RELEASE"
exit ;;
milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*)
- echo m68k-milan-mint${UNAME_RELEASE}
+ echo m68k-milan-mint"$UNAME_RELEASE"
exit ;;
hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*)
- echo m68k-hades-mint${UNAME_RELEASE}
+ echo m68k-hades-mint"$UNAME_RELEASE"
exit ;;
*:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*)
- echo m68k-unknown-mint${UNAME_RELEASE}
+ echo m68k-unknown-mint"$UNAME_RELEASE"
exit ;;
m68k:machten:*:*)
- echo m68k-apple-machten${UNAME_RELEASE}
+ echo m68k-apple-machten"$UNAME_RELEASE"
exit ;;
powerpc:machten:*:*)
- echo powerpc-apple-machten${UNAME_RELEASE}
+ echo powerpc-apple-machten"$UNAME_RELEASE"
exit ;;
RISC*:Mach:*:*)
echo mips-dec-mach_bsd4.3
exit ;;
RISC*:ULTRIX:*:*)
- echo mips-dec-ultrix${UNAME_RELEASE}
+ echo mips-dec-ultrix"$UNAME_RELEASE"
exit ;;
VAX*:ULTRIX*:*:*)
- echo vax-dec-ultrix${UNAME_RELEASE}
+ echo vax-dec-ultrix"$UNAME_RELEASE"
exit ;;
2020:CLIX:*:* | 2430:CLIX:*:*)
- echo clipper-intergraph-clix${UNAME_RELEASE}
+ echo clipper-intergraph-clix"$UNAME_RELEASE"
exit ;;
mips:*:*:UMIPS | mips:*:*:RISCos)
- eval $set_cc_for_build
- sed 's/^ //' << EOF >$dummy.c
+ eval "$set_cc_for_build"
+ sed 's/^ //' << EOF > "$dummy.c"
#ifdef __cplusplus
#include <stdio.h> /* for printf() prototype */
int main (int argc, char *argv[]) {
@@ -478,23 +492,23 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
#endif
#if defined (host_mips) && defined (MIPSEB)
#if defined (SYSTYPE_SYSV)
- printf ("mips-mips-riscos%ssysv\n", argv[1]); exit (0);
+ printf ("mips-mips-riscos%ssysv\\n", argv[1]); exit (0);
#endif
#if defined (SYSTYPE_SVR4)
- printf ("mips-mips-riscos%ssvr4\n", argv[1]); exit (0);
+ printf ("mips-mips-riscos%ssvr4\\n", argv[1]); exit (0);
#endif
#if defined (SYSTYPE_BSD43) || defined(SYSTYPE_BSD)
- printf ("mips-mips-riscos%sbsd\n", argv[1]); exit (0);
+ printf ("mips-mips-riscos%sbsd\\n", argv[1]); exit (0);
#endif
#endif
exit (-1);
}
EOF
- $CC_FOR_BUILD -o $dummy $dummy.c &&
- dummyarg=`echo "${UNAME_RELEASE}" | sed -n 's/\([0-9]*\).*/\1/p'` &&
- SYSTEM_NAME=`$dummy $dummyarg` &&
+ $CC_FOR_BUILD -o "$dummy" "$dummy.c" &&
+ dummyarg=`echo "$UNAME_RELEASE" | sed -n 's/\([0-9]*\).*/\1/p'` &&
+ SYSTEM_NAME=`"$dummy" "$dummyarg"` &&
{ echo "$SYSTEM_NAME"; exit; }
- echo mips-mips-riscos${UNAME_RELEASE}
+ echo mips-mips-riscos"$UNAME_RELEASE"
exit ;;
Motorola:PowerMAX_OS:*:*)
echo powerpc-motorola-powermax
@@ -520,17 +534,17 @@ EOF
AViiON:dgux:*:*)
# DG/UX returns AViiON for all architectures
UNAME_PROCESSOR=`/usr/bin/uname -p`
- if [ $UNAME_PROCESSOR = mc88100 ] || [ $UNAME_PROCESSOR = mc88110 ]
+ if [ "$UNAME_PROCESSOR" = mc88100 ] || [ "$UNAME_PROCESSOR" = mc88110 ]
then
- if [ ${TARGET_BINARY_INTERFACE}x = m88kdguxelfx ] || \
- [ ${TARGET_BINARY_INTERFACE}x = x ]
+ if [ "$TARGET_BINARY_INTERFACE"x = m88kdguxelfx ] || \
+ [ "$TARGET_BINARY_INTERFACE"x = x ]
then
- echo m88k-dg-dgux${UNAME_RELEASE}
+ echo m88k-dg-dgux"$UNAME_RELEASE"
else
- echo m88k-dg-dguxbcs${UNAME_RELEASE}
+ echo m88k-dg-dguxbcs"$UNAME_RELEASE"
fi
else
- echo i586-dg-dgux${UNAME_RELEASE}
+ echo i586-dg-dgux"$UNAME_RELEASE"
fi
exit ;;
M88*:DolphinOS:*:*) # DolphinOS (SVR3)
@@ -547,7 +561,7 @@ EOF
echo m68k-tektronix-bsd
exit ;;
*:IRIX*:*:*)
- echo mips-sgi-irix`echo ${UNAME_RELEASE}|sed -e 's/-/_/g'`
+ echo mips-sgi-irix"`echo "$UNAME_RELEASE"|sed -e 's/-/_/g'`"
exit ;;
????????:AIX?:[12].1:2) # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX.
echo romp-ibm-aix # uname -m gives an 8 hex-code CPU id
@@ -559,14 +573,14 @@ EOF
if [ -x /usr/bin/oslevel ] ; then
IBM_REV=`/usr/bin/oslevel`
else
- IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE}
+ IBM_REV="$UNAME_VERSION.$UNAME_RELEASE"
fi
- echo ${UNAME_MACHINE}-ibm-aix${IBM_REV}
+ echo "$UNAME_MACHINE"-ibm-aix"$IBM_REV"
exit ;;
*:AIX:2:3)
if grep bos325 /usr/include/stdio.h >/dev/null 2>&1; then
- eval $set_cc_for_build
- sed 's/^ //' << EOF >$dummy.c
+ eval "$set_cc_for_build"
+ sed 's/^ //' << EOF > "$dummy.c"
#include <sys/systemcfg.h>
main()
@@ -577,7 +591,7 @@ EOF
exit(0);
}
EOF
- if $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy`
+ if $CC_FOR_BUILD -o "$dummy" "$dummy.c" && SYSTEM_NAME=`"$dummy"`
then
echo "$SYSTEM_NAME"
else
@@ -591,7 +605,7 @@ EOF
exit ;;
*:AIX:*:[4567])
IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'`
- if /usr/sbin/lsattr -El ${IBM_CPU_ID} | grep ' POWER' >/dev/null 2>&1; then
+ if /usr/sbin/lsattr -El "$IBM_CPU_ID" | grep ' POWER' >/dev/null 2>&1; then
IBM_ARCH=rs6000
else
IBM_ARCH=powerpc
@@ -600,18 +614,18 @@ EOF
IBM_REV=`/usr/bin/lslpp -Lqc bos.rte.libc |
awk -F: '{ print $3 }' | sed s/[0-9]*$/0/`
else
- IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE}
+ IBM_REV="$UNAME_VERSION.$UNAME_RELEASE"
fi
- echo ${IBM_ARCH}-ibm-aix${IBM_REV}
+ echo "$IBM_ARCH"-ibm-aix"$IBM_REV"
exit ;;
*:AIX:*:*)
echo rs6000-ibm-aix
exit ;;
- ibmrt:4.4BSD:*|romp-ibm:BSD:*)
+ ibmrt:4.4BSD:*|romp-ibm:4.4BSD:*)
echo romp-ibm-bsd4.4
exit ;;
ibmrt:*BSD:*|romp-ibm:BSD:*) # covers RT/PC BSD and
- echo romp-ibm-bsd${UNAME_RELEASE} # 4.3 with uname added to
+ echo romp-ibm-bsd"$UNAME_RELEASE" # 4.3 with uname added to
exit ;; # report: romp-ibm BSD 4.3
*:BOSX:*:*)
echo rs6000-bull-bosx
@@ -626,28 +640,28 @@ EOF
echo m68k-hp-bsd4.4
exit ;;
9000/[34678]??:HP-UX:*:*)
- HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'`
- case "${UNAME_MACHINE}" in
- 9000/31? ) HP_ARCH=m68000 ;;
- 9000/[34]?? ) HP_ARCH=m68k ;;
+ HPUX_REV=`echo "$UNAME_RELEASE"|sed -e 's/[^.]*.[0B]*//'`
+ case "$UNAME_MACHINE" in
+ 9000/31?) HP_ARCH=m68000 ;;
+ 9000/[34]??) HP_ARCH=m68k ;;
9000/[678][0-9][0-9])
if [ -x /usr/bin/getconf ]; then
sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null`
sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null`
- case "${sc_cpu_version}" in
- 523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0
- 528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1
+ case "$sc_cpu_version" in
+ 523) HP_ARCH=hppa1.0 ;; # CPU_PA_RISC1_0
+ 528) HP_ARCH=hppa1.1 ;; # CPU_PA_RISC1_1
532) # CPU_PA_RISC2_0
- case "${sc_kernel_bits}" in
- 32) HP_ARCH="hppa2.0n" ;;
- 64) HP_ARCH="hppa2.0w" ;;
- '') HP_ARCH="hppa2.0" ;; # HP-UX 10.20
+ case "$sc_kernel_bits" in
+ 32) HP_ARCH=hppa2.0n ;;
+ 64) HP_ARCH=hppa2.0w ;;
+ '') HP_ARCH=hppa2.0 ;; # HP-UX 10.20
esac ;;
esac
fi
- if [ "${HP_ARCH}" = "" ]; then
- eval $set_cc_for_build
- sed 's/^ //' << EOF >$dummy.c
+ if [ "$HP_ARCH" = "" ]; then
+ eval "$set_cc_for_build"
+ sed 's/^ //' << EOF > "$dummy.c"
#define _HPUX_SOURCE
#include <stdlib.h>
@@ -680,13 +694,13 @@ EOF
exit (0);
}
EOF
- (CCOPTS= $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy`
+ (CCOPTS="" $CC_FOR_BUILD -o "$dummy" "$dummy.c" 2>/dev/null) && HP_ARCH=`"$dummy"`
test -z "$HP_ARCH" && HP_ARCH=hppa
fi ;;
esac
- if [ ${HP_ARCH} = "hppa2.0w" ]
+ if [ "$HP_ARCH" = hppa2.0w ]
then
- eval $set_cc_for_build
+ eval "$set_cc_for_build"
# hppa2.0w-hp-hpux* has a 64-bit kernel and a compiler generating
# 32-bit code. hppa64-hp-hpux* has the same kernel and a compiler
@@ -697,23 +711,23 @@ EOF
# $ CC_FOR_BUILD="cc +DA2.0w" ./config.guess
# => hppa64-hp-hpux11.23
- if echo __LP64__ | (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) |
+ if echo __LP64__ | (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) |
grep -q __LP64__
then
- HP_ARCH="hppa2.0w"
+ HP_ARCH=hppa2.0w
else
- HP_ARCH="hppa64"
+ HP_ARCH=hppa64
fi
fi
- echo ${HP_ARCH}-hp-hpux${HPUX_REV}
+ echo "$HP_ARCH"-hp-hpux"$HPUX_REV"
exit ;;
ia64:HP-UX:*:*)
- HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'`
- echo ia64-hp-hpux${HPUX_REV}
+ HPUX_REV=`echo "$UNAME_RELEASE"|sed -e 's/[^.]*.[0B]*//'`
+ echo ia64-hp-hpux"$HPUX_REV"
exit ;;
3050*:HI-UX:*:*)
- eval $set_cc_for_build
- sed 's/^ //' << EOF >$dummy.c
+ eval "$set_cc_for_build"
+ sed 's/^ //' << EOF > "$dummy.c"
#include <unistd.h>
int
main ()
@@ -738,11 +752,11 @@ EOF
exit (0);
}
EOF
- $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` &&
+ $CC_FOR_BUILD -o "$dummy" "$dummy.c" && SYSTEM_NAME=`"$dummy"` &&
{ echo "$SYSTEM_NAME"; exit; }
echo unknown-hitachi-hiuxwe2
exit ;;
- 9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:* )
+ 9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:*)
echo hppa1.1-hp-bsd
exit ;;
9000/8??:4.3bsd:*:*)
@@ -751,7 +765,7 @@ EOF
*9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*)
echo hppa1.0-hp-mpeix
exit ;;
- hp7??:OSF1:*:* | hp8?[79]:OSF1:*:* )
+ hp7??:OSF1:*:* | hp8?[79]:OSF1:*:*)
echo hppa1.1-hp-osf
exit ;;
hp8??:OSF1:*:*)
@@ -759,9 +773,9 @@ EOF
exit ;;
i*86:OSF1:*:*)
if [ -x /usr/sbin/sysversion ] ; then
- echo ${UNAME_MACHINE}-unknown-osf1mk
+ echo "$UNAME_MACHINE"-unknown-osf1mk
else
- echo ${UNAME_MACHINE}-unknown-osf1
+ echo "$UNAME_MACHINE"-unknown-osf1
fi
exit ;;
parisc*:Lites*:*:*)
@@ -786,127 +800,109 @@ EOF
echo c4-convex-bsd
exit ;;
CRAY*Y-MP:*:*:*)
- echo ymp-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ echo ymp-cray-unicos"$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/'
exit ;;
CRAY*[A-Z]90:*:*:*)
- echo ${UNAME_MACHINE}-cray-unicos${UNAME_RELEASE} \
+ echo "$UNAME_MACHINE"-cray-unicos"$UNAME_RELEASE" \
| sed -e 's/CRAY.*\([A-Z]90\)/\1/' \
-e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ \
-e 's/\.[^.]*$/.X/'
exit ;;
CRAY*TS:*:*:*)
- echo t90-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ echo t90-cray-unicos"$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/'
exit ;;
CRAY*T3E:*:*:*)
- echo alphaev5-cray-unicosmk${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ echo alphaev5-cray-unicosmk"$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/'
exit ;;
CRAY*SV1:*:*:*)
- echo sv1-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ echo sv1-cray-unicos"$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/'
exit ;;
*:UNICOS/mp:*:*)
- echo craynv-cray-unicosmp${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ echo craynv-cray-unicosmp"$UNAME_RELEASE" | sed -e 's/\.[^.]*$/.X/'
exit ;;
F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*)
- FUJITSU_PROC=`uname -m | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'`
- FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
- FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'`
+ FUJITSU_PROC=`uname -m | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz`
+ FUJITSU_SYS=`uname -p | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/\///'`
+ FUJITSU_REL=`echo "$UNAME_RELEASE" | sed -e 's/ /_/'`
echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
exit ;;
5000:UNIX_System_V:4.*:*)
- FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
- FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'`
+ FUJITSU_SYS=`uname -p | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/\///'`
+ FUJITSU_REL=`echo "$UNAME_RELEASE" | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/ /_/'`
echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
exit ;;
i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*)
- echo ${UNAME_MACHINE}-pc-bsdi${UNAME_RELEASE}
+ echo "$UNAME_MACHINE"-pc-bsdi"$UNAME_RELEASE"
exit ;;
sparc*:BSD/OS:*:*)
- echo sparc-unknown-bsdi${UNAME_RELEASE}
+ echo sparc-unknown-bsdi"$UNAME_RELEASE"
exit ;;
*:BSD/OS:*:*)
- echo ${UNAME_MACHINE}-unknown-bsdi${UNAME_RELEASE}
+ echo "$UNAME_MACHINE"-unknown-bsdi"$UNAME_RELEASE"
exit ;;
*:FreeBSD:*:*)
UNAME_PROCESSOR=`/usr/bin/uname -p`
- case ${UNAME_PROCESSOR} in
+ case "$UNAME_PROCESSOR" in
amd64)
- echo x86_64-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;;
- *)
- echo ${UNAME_PROCESSOR}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;;
+ UNAME_PROCESSOR=x86_64 ;;
+ i386)
+ UNAME_PROCESSOR=i586 ;;
esac
+ echo "$UNAME_PROCESSOR"-unknown-freebsd"`echo "$UNAME_RELEASE"|sed -e 's/[-(].*//'`"
exit ;;
i*:CYGWIN*:*)
- echo ${UNAME_MACHINE}-pc-cygwin
+ echo "$UNAME_MACHINE"-pc-cygwin
exit ;;
*:MINGW64*:*)
- echo ${UNAME_MACHINE}-pc-mingw64
+ echo "$UNAME_MACHINE"-pc-mingw64
exit ;;
*:MINGW*:*)
- echo ${UNAME_MACHINE}-pc-mingw32
+ echo "$UNAME_MACHINE"-pc-mingw32
exit ;;
*:MSYS*:*)
- echo ${UNAME_MACHINE}-pc-msys
- exit ;;
- i*:windows32*:*)
- # uname -m includes "-pc" on this system.
- echo ${UNAME_MACHINE}-mingw32
+ echo "$UNAME_MACHINE"-pc-msys
exit ;;
i*:PW*:*)
- echo ${UNAME_MACHINE}-pc-pw32
+ echo "$UNAME_MACHINE"-pc-pw32
exit ;;
*:Interix*:*)
- case ${UNAME_MACHINE} in
+ case "$UNAME_MACHINE" in
x86)
- echo i586-pc-interix${UNAME_RELEASE}
+ echo i586-pc-interix"$UNAME_RELEASE"
exit ;;
authenticamd | genuineintel | EM64T)
- echo x86_64-unknown-interix${UNAME_RELEASE}
+ echo x86_64-unknown-interix"$UNAME_RELEASE"
exit ;;
IA64)
- echo ia64-unknown-interix${UNAME_RELEASE}
+ echo ia64-unknown-interix"$UNAME_RELEASE"
exit ;;
esac ;;
- [345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*)
- echo i${UNAME_MACHINE}-pc-mks
- exit ;;
- 8664:Windows_NT:*)
- echo x86_64-pc-mks
- exit ;;
- i*:Windows_NT*:* | Pentium*:Windows_NT*:*)
- # How do we know it's Interix rather than the generic POSIX subsystem?
- # It also conflicts with pre-2.0 versions of AT&T UWIN. Should we
- # UNAME_MACHINE based on the output of uname instead of i386?
- echo i586-pc-interix
- exit ;;
i*:UWIN*:*)
- echo ${UNAME_MACHINE}-pc-uwin
+ echo "$UNAME_MACHINE"-pc-uwin
exit ;;
amd64:CYGWIN*:*:* | x86_64:CYGWIN*:*:*)
echo x86_64-unknown-cygwin
exit ;;
- p*:CYGWIN*:*)
- echo powerpcle-unknown-cygwin
- exit ;;
prep*:SunOS:5.*:*)
- echo powerpcle-unknown-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ echo powerpcle-unknown-solaris2"`echo "$UNAME_RELEASE"|sed -e 's/[^.]*//'`"
exit ;;
*:GNU:*:*)
# the GNU system
- echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-${LIBC}`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'`
+ echo "`echo "$UNAME_MACHINE"|sed -e 's,[-/].*$,,'`-unknown-$LIBC`echo "$UNAME_RELEASE"|sed -e 's,/.*$,,'`"
exit ;;
*:GNU/*:*:*)
# other systems with GNU libc and userland
- echo ${UNAME_MACHINE}-unknown-`echo ${UNAME_SYSTEM} | sed 's,^[^/]*/,,' | tr '[A-Z]' '[a-z]'``echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`-${LIBC}
+ echo "$UNAME_MACHINE-unknown-`echo "$UNAME_SYSTEM" | sed 's,^[^/]*/,,' | tr "[:upper:]" "[:lower:]"``echo "$UNAME_RELEASE"|sed -e 's/[-(].*//'`-$LIBC"
exit ;;
i*86:Minix:*:*)
- echo ${UNAME_MACHINE}-pc-minix
+ echo "$UNAME_MACHINE"-pc-minix
exit ;;
aarch64:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
aarch64_be:Linux:*:*)
UNAME_MACHINE=aarch64_be
- echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
alpha:Linux:*:*)
case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in
@@ -919,61 +915,64 @@ EOF
EV68*) UNAME_MACHINE=alphaev68 ;;
esac
objdump --private-headers /bin/sh | grep -q ld.so.1
- if test "$?" = 0 ; then LIBC="gnulibc1" ; fi
- echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ if test "$?" = 0 ; then LIBC=gnulibc1 ; fi
+ echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
arc:Linux:*:* | arceb:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
arm*:Linux:*:*)
- eval $set_cc_for_build
+ eval "$set_cc_for_build"
if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \
| grep -q __ARM_EABI__
then
- echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
else
if echo __ARM_PCS_VFP | $CC_FOR_BUILD -E - 2>/dev/null \
| grep -q __ARM_PCS_VFP
then
- echo ${UNAME_MACHINE}-unknown-linux-${LIBC}eabi
+ echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"eabi
else
- echo ${UNAME_MACHINE}-unknown-linux-${LIBC}eabihf
+ echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"eabihf
fi
fi
exit ;;
avr32*:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
cris:Linux:*:*)
- echo ${UNAME_MACHINE}-axis-linux-${LIBC}
+ echo "$UNAME_MACHINE"-axis-linux-"$LIBC"
exit ;;
crisv32:Linux:*:*)
- echo ${UNAME_MACHINE}-axis-linux-${LIBC}
+ echo "$UNAME_MACHINE"-axis-linux-"$LIBC"
exit ;;
e2k:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
frv:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
hexagon:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
i*86:Linux:*:*)
- echo ${UNAME_MACHINE}-pc-linux-${LIBC}
+ echo "$UNAME_MACHINE"-pc-linux-"$LIBC"
exit ;;
ia64:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
+ exit ;;
+ k1om:Linux:*:*)
+ echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
m32r*:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
m68*:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
mips:Linux:*:* | mips64:Linux:*:*)
- eval $set_cc_for_build
- sed 's/^ //' << EOF >$dummy.c
+ eval "$set_cc_for_build"
+ sed 's/^ //' << EOF > "$dummy.c"
#undef CPU
#undef ${UNAME_MACHINE}
#undef ${UNAME_MACHINE}el
@@ -987,64 +986,74 @@ EOF
#endif
#endif
EOF
- eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^CPU'`
- test x"${CPU}" != x && { echo "${CPU}-unknown-linux-${LIBC}"; exit; }
+ eval "`$CC_FOR_BUILD -E "$dummy.c" 2>/dev/null | grep '^CPU'`"
+ test "x$CPU" != x && { echo "$CPU-unknown-linux-$LIBC"; exit; }
;;
+ mips64el:Linux:*:*)
+ echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
+ exit ;;
openrisc*:Linux:*:*)
- echo or1k-unknown-linux-${LIBC}
+ echo or1k-unknown-linux-"$LIBC"
exit ;;
or32:Linux:*:* | or1k*:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
padre:Linux:*:*)
- echo sparc-unknown-linux-${LIBC}
+ echo sparc-unknown-linux-"$LIBC"
exit ;;
parisc64:Linux:*:* | hppa64:Linux:*:*)
- echo hppa64-unknown-linux-${LIBC}
+ echo hppa64-unknown-linux-"$LIBC"
exit ;;
parisc:Linux:*:* | hppa:Linux:*:*)
# Look for CPU level
case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in
- PA7*) echo hppa1.1-unknown-linux-${LIBC} ;;
- PA8*) echo hppa2.0-unknown-linux-${LIBC} ;;
- *) echo hppa-unknown-linux-${LIBC} ;;
+ PA7*) echo hppa1.1-unknown-linux-"$LIBC" ;;
+ PA8*) echo hppa2.0-unknown-linux-"$LIBC" ;;
+ *) echo hppa-unknown-linux-"$LIBC" ;;
esac
exit ;;
ppc64:Linux:*:*)
- echo powerpc64-unknown-linux-${LIBC}
+ echo powerpc64-unknown-linux-"$LIBC"
exit ;;
ppc:Linux:*:*)
- echo powerpc-unknown-linux-${LIBC}
+ echo powerpc-unknown-linux-"$LIBC"
exit ;;
ppc64le:Linux:*:*)
- echo powerpc64le-unknown-linux-${LIBC}
+ echo powerpc64le-unknown-linux-"$LIBC"
exit ;;
ppcle:Linux:*:*)
- echo powerpcle-unknown-linux-${LIBC}
+ echo powerpcle-unknown-linux-"$LIBC"
+ exit ;;
+ riscv32:Linux:*:* | riscv64:Linux:*:*)
+ echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
s390:Linux:*:* | s390x:Linux:*:*)
- echo ${UNAME_MACHINE}-ibm-linux-${LIBC}
+ echo "$UNAME_MACHINE"-ibm-linux-"$LIBC"
exit ;;
sh64*:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
sh*:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
sparc:Linux:*:* | sparc64:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
tile*:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
vax:Linux:*:*)
- echo ${UNAME_MACHINE}-dec-linux-${LIBC}
+ echo "$UNAME_MACHINE"-dec-linux-"$LIBC"
exit ;;
x86_64:Linux:*:*)
- echo ${UNAME_MACHINE}-pc-linux-${LIBC}
+ if objdump -f /bin/sh | grep -q elf32-x86-64; then
+ echo "$UNAME_MACHINE"-pc-linux-"$LIBC"x32
+ else
+ echo "$UNAME_MACHINE"-pc-linux-"$LIBC"
+ fi
exit ;;
xtensa*:Linux:*:*)
- echo ${UNAME_MACHINE}-unknown-linux-${LIBC}
+ echo "$UNAME_MACHINE"-unknown-linux-"$LIBC"
exit ;;
i*86:DYNIX/ptx:4*:*)
# ptx 4.0 does uname -s correctly, with DYNIX/ptx in there.
@@ -1058,34 +1067,34 @@ EOF
# I am not positive that other SVR4 systems won't match this,
# I just have to hope. -- rms.
# Use sysv4.2uw... so that sysv4* matches it.
- echo ${UNAME_MACHINE}-pc-sysv4.2uw${UNAME_VERSION}
+ echo "$UNAME_MACHINE"-pc-sysv4.2uw"$UNAME_VERSION"
exit ;;
i*86:OS/2:*:*)
# If we were able to find `uname', then EMX Unix compatibility
# is probably installed.
- echo ${UNAME_MACHINE}-pc-os2-emx
+ echo "$UNAME_MACHINE"-pc-os2-emx
exit ;;
i*86:XTS-300:*:STOP)
- echo ${UNAME_MACHINE}-unknown-stop
+ echo "$UNAME_MACHINE"-unknown-stop
exit ;;
i*86:atheos:*:*)
- echo ${UNAME_MACHINE}-unknown-atheos
+ echo "$UNAME_MACHINE"-unknown-atheos
exit ;;
i*86:syllable:*:*)
- echo ${UNAME_MACHINE}-pc-syllable
+ echo "$UNAME_MACHINE"-pc-syllable
exit ;;
i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.[02]*:*)
- echo i386-unknown-lynxos${UNAME_RELEASE}
+ echo i386-unknown-lynxos"$UNAME_RELEASE"
exit ;;
i*86:*DOS:*:*)
- echo ${UNAME_MACHINE}-pc-msdosdjgpp
+ echo "$UNAME_MACHINE"-pc-msdosdjgpp
exit ;;
- i*86:*:4.*:* | i*86:SYSTEM_V:4.*:*)
- UNAME_REL=`echo ${UNAME_RELEASE} | sed 's/\/MP$//'`
+ i*86:*:4.*:*)
+ UNAME_REL=`echo "$UNAME_RELEASE" | sed 's/\/MP$//'`
if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then
- echo ${UNAME_MACHINE}-univel-sysv${UNAME_REL}
+ echo "$UNAME_MACHINE"-univel-sysv"$UNAME_REL"
else
- echo ${UNAME_MACHINE}-pc-sysv${UNAME_REL}
+ echo "$UNAME_MACHINE"-pc-sysv"$UNAME_REL"
fi
exit ;;
i*86:*:5:[678]*)
@@ -1095,12 +1104,12 @@ EOF
*Pentium) UNAME_MACHINE=i586 ;;
*Pent*|*Celeron) UNAME_MACHINE=i686 ;;
esac
- echo ${UNAME_MACHINE}-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION}
+ echo "$UNAME_MACHINE-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}{$UNAME_VERSION}"
exit ;;
i*86:*:3.2:*)
if test -f /usr/options/cb.name; then
UNAME_REL=`sed -n 's/.*Version //p' </usr/options/cb.name`
- echo ${UNAME_MACHINE}-pc-isc$UNAME_REL
+ echo "$UNAME_MACHINE"-pc-isc"$UNAME_REL"
elif /bin/uname -X 2>/dev/null >/dev/null ; then
UNAME_REL=`(/bin/uname -X|grep Release|sed -e 's/.*= //')`
(/bin/uname -X|grep i80486 >/dev/null) && UNAME_MACHINE=i486
@@ -1110,9 +1119,9 @@ EOF
&& UNAME_MACHINE=i686
(/bin/uname -X|grep '^Machine.*Pentium Pro' >/dev/null) \
&& UNAME_MACHINE=i686
- echo ${UNAME_MACHINE}-pc-sco$UNAME_REL
+ echo "$UNAME_MACHINE"-pc-sco"$UNAME_REL"
else
- echo ${UNAME_MACHINE}-pc-sysv32
+ echo "$UNAME_MACHINE"-pc-sysv32
fi
exit ;;
pc:*:*:*)
@@ -1120,7 +1129,7 @@ EOF
# uname -m prints for DJGPP always 'pc', but it prints nothing about
# the processor, so we play safe by assuming i586.
# Note: whatever this is, it MUST be the same as what config.sub
- # prints for the "djgpp" host, or else GDB configury will decide that
+ # prints for the "djgpp" host, or else GDB configure will decide that
# this is a cross-build.
echo i586-pc-msdosdjgpp
exit ;;
@@ -1132,9 +1141,9 @@ EOF
exit ;;
i860:*:4.*:*) # i860-SVR4
if grep Stardent /usr/include/sys/uadmin.h >/dev/null 2>&1 ; then
- echo i860-stardent-sysv${UNAME_RELEASE} # Stardent Vistra i860-SVR4
+ echo i860-stardent-sysv"$UNAME_RELEASE" # Stardent Vistra i860-SVR4
else # Add other i860-SVR4 vendors below as they are discovered.
- echo i860-unknown-sysv${UNAME_RELEASE} # Unknown i860-SVR4
+ echo i860-unknown-sysv"$UNAME_RELEASE" # Unknown i860-SVR4
fi
exit ;;
mini*:CTIX:SYS*5:*)
@@ -1154,9 +1163,9 @@ EOF
test -r /etc/.relid \
&& OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid`
/bin/uname -p 2>/dev/null | grep 86 >/dev/null \
- && { echo i486-ncr-sysv4.3${OS_REL}; exit; }
+ && { echo i486-ncr-sysv4.3"$OS_REL"; exit; }
/bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \
- && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;;
+ && { echo i586-ncr-sysv4.3"$OS_REL"; exit; } ;;
3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*)
/bin/uname -p 2>/dev/null | grep 86 >/dev/null \
&& { echo i486-ncr-sysv4; exit; } ;;
@@ -1165,28 +1174,28 @@ EOF
test -r /etc/.relid \
&& OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid`
/bin/uname -p 2>/dev/null | grep 86 >/dev/null \
- && { echo i486-ncr-sysv4.3${OS_REL}; exit; }
+ && { echo i486-ncr-sysv4.3"$OS_REL"; exit; }
/bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \
- && { echo i586-ncr-sysv4.3${OS_REL}; exit; }
+ && { echo i586-ncr-sysv4.3"$OS_REL"; exit; }
/bin/uname -p 2>/dev/null | /bin/grep pteron >/dev/null \
- && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;;
+ && { echo i586-ncr-sysv4.3"$OS_REL"; exit; } ;;
m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*)
- echo m68k-unknown-lynxos${UNAME_RELEASE}
+ echo m68k-unknown-lynxos"$UNAME_RELEASE"
exit ;;
mc68030:UNIX_System_V:4.*:*)
echo m68k-atari-sysv4
exit ;;
TSUNAMI:LynxOS:2.*:*)
- echo sparc-unknown-lynxos${UNAME_RELEASE}
+ echo sparc-unknown-lynxos"$UNAME_RELEASE"
exit ;;
rs6000:LynxOS:2.*:*)
- echo rs6000-unknown-lynxos${UNAME_RELEASE}
+ echo rs6000-unknown-lynxos"$UNAME_RELEASE"
exit ;;
PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.[02]*:*)
- echo powerpc-unknown-lynxos${UNAME_RELEASE}
+ echo powerpc-unknown-lynxos"$UNAME_RELEASE"
exit ;;
SM[BE]S:UNIX_SV:*:*)
- echo mips-dde-sysv${UNAME_RELEASE}
+ echo mips-dde-sysv"$UNAME_RELEASE"
exit ;;
RM*:ReliantUNIX-*:*:*)
echo mips-sni-sysv4
@@ -1197,7 +1206,7 @@ EOF
*:SINIX-*:*:*)
if uname -p 2>/dev/null >/dev/null ; then
UNAME_MACHINE=`(uname -p) 2>/dev/null`
- echo ${UNAME_MACHINE}-sni-sysv4
+ echo "$UNAME_MACHINE"-sni-sysv4
else
echo ns32k-sni-sysv
fi
@@ -1217,23 +1226,23 @@ EOF
exit ;;
i*86:VOS:*:*)
# From Paul.Green at stratus.com.
- echo ${UNAME_MACHINE}-stratus-vos
+ echo "$UNAME_MACHINE"-stratus-vos
exit ;;
*:VOS:*:*)
# From Paul.Green at stratus.com.
echo hppa1.1-stratus-vos
exit ;;
mc68*:A/UX:*:*)
- echo m68k-apple-aux${UNAME_RELEASE}
+ echo m68k-apple-aux"$UNAME_RELEASE"
exit ;;
news*:NEWS-OS:6*:*)
echo mips-sony-newsos6
exit ;;
R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*)
if [ -d /usr/nec ]; then
- echo mips-nec-sysv${UNAME_RELEASE}
+ echo mips-nec-sysv"$UNAME_RELEASE"
else
- echo mips-unknown-sysv${UNAME_RELEASE}
+ echo mips-unknown-sysv"$UNAME_RELEASE"
fi
exit ;;
BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only.
@@ -1252,46 +1261,56 @@ EOF
echo x86_64-unknown-haiku
exit ;;
SX-4:SUPER-UX:*:*)
- echo sx4-nec-superux${UNAME_RELEASE}
+ echo sx4-nec-superux"$UNAME_RELEASE"
exit ;;
SX-5:SUPER-UX:*:*)
- echo sx5-nec-superux${UNAME_RELEASE}
+ echo sx5-nec-superux"$UNAME_RELEASE"
exit ;;
SX-6:SUPER-UX:*:*)
- echo sx6-nec-superux${UNAME_RELEASE}
+ echo sx6-nec-superux"$UNAME_RELEASE"
exit ;;
SX-7:SUPER-UX:*:*)
- echo sx7-nec-superux${UNAME_RELEASE}
+ echo sx7-nec-superux"$UNAME_RELEASE"
exit ;;
SX-8:SUPER-UX:*:*)
- echo sx8-nec-superux${UNAME_RELEASE}
+ echo sx8-nec-superux"$UNAME_RELEASE"
exit ;;
SX-8R:SUPER-UX:*:*)
- echo sx8r-nec-superux${UNAME_RELEASE}
+ echo sx8r-nec-superux"$UNAME_RELEASE"
+ exit ;;
+ SX-ACE:SUPER-UX:*:*)
+ echo sxace-nec-superux"$UNAME_RELEASE"
exit ;;
Power*:Rhapsody:*:*)
- echo powerpc-apple-rhapsody${UNAME_RELEASE}
+ echo powerpc-apple-rhapsody"$UNAME_RELEASE"
exit ;;
*:Rhapsody:*:*)
- echo ${UNAME_MACHINE}-apple-rhapsody${UNAME_RELEASE}
+ echo "$UNAME_MACHINE"-apple-rhapsody"$UNAME_RELEASE"
exit ;;
*:Darwin:*:*)
UNAME_PROCESSOR=`uname -p` || UNAME_PROCESSOR=unknown
- eval $set_cc_for_build
+ eval "$set_cc_for_build"
if test "$UNAME_PROCESSOR" = unknown ; then
UNAME_PROCESSOR=powerpc
fi
- if test `echo "$UNAME_RELEASE" | sed -e 's/\..*//'` -le 10 ; then
- if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then
+ if test "`echo "$UNAME_RELEASE" | sed -e 's/\..*//'`" -le 10 ; then
+ if [ "$CC_FOR_BUILD" != no_compiler_found ]; then
if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \
- (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \
- grep IS_64BIT_ARCH >/dev/null
+ (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \
+ grep IS_64BIT_ARCH >/dev/null
then
case $UNAME_PROCESSOR in
i386) UNAME_PROCESSOR=x86_64 ;;
powerpc) UNAME_PROCESSOR=powerpc64 ;;
esac
fi
+ # On 10.4-10.6 one might compile for PowerPC via gcc -arch ppc
+ if (echo '#ifdef __POWERPC__'; echo IS_PPC; echo '#endif') | \
+ (CCOPTS="" $CC_FOR_BUILD -E - 2>/dev/null) | \
+ grep IS_PPC >/dev/null
+ then
+ UNAME_PROCESSOR=powerpc
+ fi
fi
elif test "$UNAME_PROCESSOR" = i386 ; then
# Avoid executing cc on OS X 10.9, as it ships with a stub
@@ -1302,27 +1321,33 @@ EOF
# that Apple uses in portable devices.
UNAME_PROCESSOR=x86_64
fi
- echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE}
+ echo "$UNAME_PROCESSOR"-apple-darwin"$UNAME_RELEASE"
exit ;;
*:procnto*:*:* | *:QNX:[0123456789]*:*)
UNAME_PROCESSOR=`uname -p`
- if test "$UNAME_PROCESSOR" = "x86"; then
+ if test "$UNAME_PROCESSOR" = x86; then
UNAME_PROCESSOR=i386
UNAME_MACHINE=pc
fi
- echo ${UNAME_PROCESSOR}-${UNAME_MACHINE}-nto-qnx${UNAME_RELEASE}
+ echo "$UNAME_PROCESSOR"-"$UNAME_MACHINE"-nto-qnx"$UNAME_RELEASE"
exit ;;
*:QNX:*:4*)
echo i386-pc-qnx
exit ;;
- NEO-?:NONSTOP_KERNEL:*:*)
- echo neo-tandem-nsk${UNAME_RELEASE}
+ NEO-*:NONSTOP_KERNEL:*:*)
+ echo neo-tandem-nsk"$UNAME_RELEASE"
exit ;;
NSE-*:NONSTOP_KERNEL:*:*)
- echo nse-tandem-nsk${UNAME_RELEASE}
+ echo nse-tandem-nsk"$UNAME_RELEASE"
+ exit ;;
+ NSR-*:NONSTOP_KERNEL:*:*)
+ echo nsr-tandem-nsk"$UNAME_RELEASE"
exit ;;
- NSR-?:NONSTOP_KERNEL:*:*)
- echo nsr-tandem-nsk${UNAME_RELEASE}
+ NSV-*:NONSTOP_KERNEL:*:*)
+ echo nsv-tandem-nsk"$UNAME_RELEASE"
+ exit ;;
+ NSX-*:NONSTOP_KERNEL:*:*)
+ echo nsx-tandem-nsk"$UNAME_RELEASE"
exit ;;
*:NonStop-UX:*:*)
echo mips-compaq-nonstopux
@@ -1331,18 +1356,18 @@ EOF
echo bs2000-siemens-sysv
exit ;;
DS/*:UNIX_System_V:*:*)
- echo ${UNAME_MACHINE}-${UNAME_SYSTEM}-${UNAME_RELEASE}
+ echo "$UNAME_MACHINE"-"$UNAME_SYSTEM"-"$UNAME_RELEASE"
exit ;;
*:Plan9:*:*)
# "uname -m" is not consistent, so use $cputype instead. 386
# is converted to i386 for consistency with other x86
# operating systems.
- if test "$cputype" = "386"; then
+ if test "$cputype" = 386; then
UNAME_MACHINE=i386
else
UNAME_MACHINE="$cputype"
fi
- echo ${UNAME_MACHINE}-unknown-plan9
+ echo "$UNAME_MACHINE"-unknown-plan9
exit ;;
*:TOPS-10:*:*)
echo pdp10-unknown-tops10
@@ -1363,14 +1388,14 @@ EOF
echo pdp10-unknown-its
exit ;;
SEI:*:*:SEIUX)
- echo mips-sei-seiux${UNAME_RELEASE}
+ echo mips-sei-seiux"$UNAME_RELEASE"
exit ;;
*:DragonFly:*:*)
- echo ${UNAME_MACHINE}-unknown-dragonfly`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`
+ echo "$UNAME_MACHINE"-unknown-dragonfly"`echo "$UNAME_RELEASE"|sed -e 's/[-(].*//'`"
exit ;;
*:*VMS:*:*)
UNAME_MACHINE=`(uname -p) 2>/dev/null`
- case "${UNAME_MACHINE}" in
+ case "$UNAME_MACHINE" in
A*) echo alpha-dec-vms ; exit ;;
I*) echo ia64-dec-vms ; exit ;;
V*) echo vax-dec-vms ; exit ;;
@@ -1379,34 +1404,48 @@ EOF
echo i386-pc-xenix
exit ;;
i*86:skyos:*:*)
- echo ${UNAME_MACHINE}-pc-skyos`echo ${UNAME_RELEASE}` | sed -e 's/ .*$//'
+ echo "$UNAME_MACHINE"-pc-skyos"`echo "$UNAME_RELEASE" | sed -e 's/ .*$//'`"
exit ;;
i*86:rdos:*:*)
- echo ${UNAME_MACHINE}-pc-rdos
+ echo "$UNAME_MACHINE"-pc-rdos
exit ;;
i*86:AROS:*:*)
- echo ${UNAME_MACHINE}-pc-aros
+ echo "$UNAME_MACHINE"-pc-aros
exit ;;
x86_64:VMkernel:*:*)
- echo ${UNAME_MACHINE}-unknown-esx
+ echo "$UNAME_MACHINE"-unknown-esx
+ exit ;;
+ amd64:Isilon\ OneFS:*:*)
+ echo x86_64-unknown-onefs
exit ;;
esac
+echo "$0: unable to guess system type" >&2
+
+case "$UNAME_MACHINE:$UNAME_SYSTEM" in
+ mips:Linux | mips64:Linux)
+ # If we got here on MIPS GNU/Linux, output extra information.
+ cat >&2 <<EOF
+
+NOTE: MIPS GNU/Linux systems require a C compiler to fully recognize
+the system type. Please install a C compiler and try again.
+EOF
+ ;;
+esac
+
cat >&2 <<EOF
-$0: unable to guess system type
-This script, last modified $timestamp, has failed to recognize
-the operating system you are using. It is advised that you
-download the most up to date version of the config scripts from
+This script (version $timestamp), has failed to recognize the
+operating system you are using. If your script is old, overwrite *all*
+copies of config.guess and config.sub with the latest versions from:
- http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD
+ https://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess
and
- http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD
+ https://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub
-If the version you run ($0) is already up to date, please
-send the following data and any information you think might be
-pertinent to <config-patches at gnu.org> in order to provide the needed
-information to handle your system.
+If $0 has already been updated, send the following data and any
+information you think might be pertinent to config-patches at gnu.org to
+provide the necessary information to handle your system.
config.guess timestamp = $timestamp
@@ -1425,16 +1464,16 @@ hostinfo = `(hostinfo) 2>/dev/null`
/usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null`
/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null`
-UNAME_MACHINE = ${UNAME_MACHINE}
-UNAME_RELEASE = ${UNAME_RELEASE}
-UNAME_SYSTEM = ${UNAME_SYSTEM}
-UNAME_VERSION = ${UNAME_VERSION}
+UNAME_MACHINE = "$UNAME_MACHINE"
+UNAME_RELEASE = "$UNAME_RELEASE"
+UNAME_SYSTEM = "$UNAME_SYSTEM"
+UNAME_VERSION = "$UNAME_VERSION"
EOF
exit 1
# Local variables:
-# eval: (add-hook 'write-file-hooks 'time-stamp)
+# eval: (add-hook 'write-file-functions 'time-stamp)
# time-stamp-start: "timestamp='"
# time-stamp-format: "%:y-%02m-%02d"
# time-stamp-end: "'"
=====================================
config.sub
=====================================
@@ -1,8 +1,8 @@
#! /bin/sh
# Configuration validation subroutine script.
-# Copyright 1992-2015 Free Software Foundation, Inc.
+# Copyright 1992-2018 Free Software Foundation, Inc.
-timestamp='2015-08-20'
+timestamp='2018-02-22'
# This file is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
@@ -15,7 +15,7 @@ timestamp='2015-08-20'
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
-# along with this program; if not, see <http://www.gnu.org/licenses/>.
+# along with this program; if not, see <https://www.gnu.org/licenses/>.
#
# As a special exception to the GNU General Public License, if you
# distribute this file as part of a program that contains a
@@ -33,7 +33,7 @@ timestamp='2015-08-20'
# Otherwise, we print the canonical config type on stdout and succeed.
# You can get the latest version of this script from:
-# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD
+# https://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub
# This file is supposed to be the same for all GNU packages
# and recognize all the CPU types, system types and aliases
@@ -53,12 +53,11 @@ timestamp='2015-08-20'
me=`echo "$0" | sed -e 's,.*/,,'`
usage="\
-Usage: $0 [OPTION] CPU-MFR-OPSYS
- $0 [OPTION] ALIAS
+Usage: $0 [OPTION] CPU-MFR-OPSYS or ALIAS
Canonicalize a configuration name.
-Operation modes:
+Options:
-h, --help print this help, then exit
-t, --time-stamp print date of last modification, then exit
-v, --version print version number, then exit
@@ -68,7 +67,7 @@ Report bugs and patches to <config-patches at gnu.org>."
version="\
GNU config.sub ($timestamp)
-Copyright 1992-2015 Free Software Foundation, Inc.
+Copyright 1992-2018 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
@@ -95,7 +94,7 @@ while test $# -gt 0 ; do
*local*)
# First pass through any local machine types.
- echo $1
+ echo "$1"
exit ;;
* )
@@ -113,24 +112,24 @@ esac
# Separate what the user gave into CPU-COMPANY and OS or KERNEL-OS (if any).
# Here we must recognize all the valid KERNEL-OS combinations.
-maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'`
+maybe_os=`echo "$1" | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'`
case $maybe_os in
nto-qnx* | linux-gnu* | linux-android* | linux-dietlibc | linux-newlib* | \
linux-musl* | linux-uclibc* | uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | \
knetbsd*-gnu* | netbsd*-gnu* | netbsd*-eabi* | \
- kopensolaris*-gnu* | \
+ kopensolaris*-gnu* | cloudabi*-eabi* | \
storm-chaos* | os2-emx* | rtmk-nova*)
os=-$maybe_os
- basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`
+ basic_machine=`echo "$1" | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`
;;
android-linux)
os=-linux-android
- basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`-unknown
+ basic_machine=`echo "$1" | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`-unknown
;;
*)
- basic_machine=`echo $1 | sed 's/-[^-]*$//'`
- if [ $basic_machine != $1 ]
- then os=`echo $1 | sed 's/.*-/-/'`
+ basic_machine=`echo "$1" | sed 's/-[^-]*$//'`
+ if [ "$basic_machine" != "$1" ]
+ then os=`echo "$1" | sed 's/.*-/-/'`
else os=; fi
;;
esac
@@ -179,44 +178,44 @@ case $os in
;;
-sco6)
os=-sco5v6
- basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
;;
-sco5)
os=-sco3.2v5
- basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
;;
-sco4)
os=-sco3.2v4
- basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
;;
-sco3.2.[4-9]*)
os=`echo $os | sed -e 's/sco3.2./sco3.2v/'`
- basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
;;
-sco3.2v[4-9]*)
# Don't forget version if it is 3.2v4 or newer.
- basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
;;
-sco5v6*)
# Don't forget version if it is 3.2v4 or newer.
- basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
;;
-sco*)
os=-sco3.2v2
- basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
;;
-udk*)
- basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
;;
-isc)
os=-isc2.2
- basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
;;
-clix*)
basic_machine=clipper-intergraph
;;
-isc*)
- basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
;;
-lynx*178)
os=-lynxos178
@@ -228,10 +227,7 @@ case $os in
os=-lynxos
;;
-ptx*)
- basic_machine=`echo $1 | sed -e 's/86-.*/86-sequent/'`
- ;;
- -windowsnt*)
- os=`echo $os | sed -e 's/windowsnt/winnt/'`
+ basic_machine=`echo "$1" | sed -e 's/86-.*/86-sequent/'`
;;
-psos*)
os=-psos
@@ -264,7 +260,7 @@ case $basic_machine in
| fido | fr30 | frv | ft32 \
| h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \
| hexagon \
- | i370 | i860 | i960 | ia64 \
+ | i370 | i860 | i960 | ia16 | ia64 \
| ip2k | iq2000 \
| k1om \
| le32 | le64 \
@@ -300,8 +296,9 @@ case $basic_machine in
| nios | nios2 | nios2eb | nios2el \
| ns16k | ns32k \
| open8 | or1k | or1knd | or32 \
- | pdp10 | pdp11 | pj | pjl \
+ | pdp10 | pj | pjl \
| powerpc | powerpc64 | powerpc64le | powerpcle \
+ | pru \
| pyramid \
| riscv32 | riscv64 \
| rl78 | rx \
@@ -315,7 +312,7 @@ case $basic_machine in
| ubicom32 \
| v850 | v850e | v850e1 | v850e2 | v850es | v850e2v3 \
| visium \
- | we32k \
+ | wasm32 \
| x86 | xc16x | xstormy16 | xtensa \
| z8k | z80)
basic_machine=$basic_machine-unknown
@@ -336,7 +333,7 @@ case $basic_machine in
basic_machine=$basic_machine-unknown
os=-none
;;
- m88110 | m680[12346]0 | m683?2 | m68360 | m5200 | v70 | w65 | z8k)
+ m88110 | m680[12346]0 | m683?2 | m68360 | m5200 | v70 | w65)
;;
ms1)
basic_machine=mt-unknown
@@ -365,7 +362,7 @@ case $basic_machine in
;;
# Object if more than one company name word.
*-*-*)
- echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2
+ echo Invalid configuration \`"$1"\': machine \`"$basic_machine"\' not recognized 1>&2
exit 1
;;
# Recognize the basic CPU types with company name.
@@ -388,7 +385,7 @@ case $basic_machine in
| h8300-* | h8500-* \
| hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \
| hexagon-* \
- | i*86-* | i860-* | i960-* | ia64-* \
+ | i*86-* | i860-* | i960-* | ia16-* | ia64-* \
| ip2k-* | iq2000-* \
| k1om-* \
| le32-* | le64-* \
@@ -429,6 +426,7 @@ case $basic_machine in
| orion-* \
| pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \
| powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* \
+ | pru-* \
| pyramid-* \
| riscv32-* | riscv64-* \
| rl78-* | romp-* | rs6000-* | rx-* \
@@ -445,6 +443,7 @@ case $basic_machine in
| v850-* | v850e-* | v850e1-* | v850es-* | v850e2-* | v850e2v3-* \
| vax-* \
| visium-* \
+ | wasm32-* \
| we32k-* \
| x86-* | x86_64-* | xc16x-* | xps100-* \
| xstormy16-* | xtensa*-* \
@@ -458,7 +457,7 @@ case $basic_machine in
# Recognize the various machine names and aliases which stand
# for a CPU type and a company and sometimes even an OS.
386bsd)
- basic_machine=i386-unknown
+ basic_machine=i386-pc
os=-bsd
;;
3b1 | 7300 | 7300-att | att-7300 | pc7300 | safari | unixpc)
@@ -492,7 +491,7 @@ case $basic_machine in
basic_machine=x86_64-pc
;;
amd64-*)
- basic_machine=x86_64-`echo $basic_machine | sed 's/^[^-]*-//'`
+ basic_machine=x86_64-`echo "$basic_machine" | sed 's/^[^-]*-//'`
;;
amdahl)
basic_machine=580-amdahl
@@ -521,7 +520,7 @@ case $basic_machine in
basic_machine=i386-pc
os=-aros
;;
- asmjs)
+ asmjs)
basic_machine=asmjs-unknown
;;
aux)
@@ -537,7 +536,7 @@ case $basic_machine in
os=-linux
;;
blackfin-*)
- basic_machine=bfin-`echo $basic_machine | sed 's/^[^-]*-//'`
+ basic_machine=bfin-`echo "$basic_machine" | sed 's/^[^-]*-//'`
os=-linux
;;
bluegene*)
@@ -545,13 +544,13 @@ case $basic_machine in
os=-cnk
;;
c54x-*)
- basic_machine=tic54x-`echo $basic_machine | sed 's/^[^-]*-//'`
+ basic_machine=tic54x-`echo "$basic_machine" | sed 's/^[^-]*-//'`
;;
c55x-*)
- basic_machine=tic55x-`echo $basic_machine | sed 's/^[^-]*-//'`
+ basic_machine=tic55x-`echo "$basic_machine" | sed 's/^[^-]*-//'`
;;
c6x-*)
- basic_machine=tic6x-`echo $basic_machine | sed 's/^[^-]*-//'`
+ basic_machine=tic6x-`echo "$basic_machine" | sed 's/^[^-]*-//'`
;;
c90)
basic_machine=c90-cray
@@ -640,10 +639,18 @@ case $basic_machine in
basic_machine=rs6000-bull
os=-bosx
;;
- dpx2* | dpx2*-bull)
+ dpx2*)
basic_machine=m68k-bull
os=-sysv3
;;
+ e500v[12])
+ basic_machine=powerpc-unknown
+ os=$os"spe"
+ ;;
+ e500v[12]-*)
+ basic_machine=powerpc-`echo "$basic_machine" | sed 's/^[^-]*-//'`
+ os=$os"spe"
+ ;;
ebmon29k)
basic_machine=a29k-amd
os=-ebmon
@@ -733,9 +740,6 @@ case $basic_machine in
hp9k8[0-9][0-9] | hp8[0-9][0-9])
basic_machine=hppa1.0-hp
;;
- hppa-next)
- os=-nextstep3
- ;;
hppaosf)
basic_machine=hppa1.1-hp
os=-osf
@@ -748,26 +752,26 @@ case $basic_machine in
basic_machine=i370-ibm
;;
i*86v32)
- basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
+ basic_machine=`echo "$1" | sed -e 's/86.*/86-pc/'`
os=-sysv32
;;
i*86v4*)
- basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
+ basic_machine=`echo "$1" | sed -e 's/86.*/86-pc/'`
os=-sysv4
;;
i*86v)
- basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
+ basic_machine=`echo "$1" | sed -e 's/86.*/86-pc/'`
os=-sysv
;;
i*86sol2)
- basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
+ basic_machine=`echo "$1" | sed -e 's/86.*/86-pc/'`
os=-solaris2
;;
i386mach)
basic_machine=i386-mach
os=-mach
;;
- i386-vsta | vsta)
+ vsta)
basic_machine=i386-unknown
os=-vsta
;;
@@ -786,19 +790,16 @@ case $basic_machine in
os=-sysv
;;
leon-*|leon[3-9]-*)
- basic_machine=sparc-`echo $basic_machine | sed 's/-.*//'`
+ basic_machine=sparc-`echo "$basic_machine" | sed 's/-.*//'`
;;
m68knommu)
basic_machine=m68k-unknown
os=-linux
;;
m68knommu-*)
- basic_machine=m68k-`echo $basic_machine | sed 's/^[^-]*-//'`
+ basic_machine=m68k-`echo "$basic_machine" | sed 's/^[^-]*-//'`
os=-linux
;;
- m88k-omron*)
- basic_machine=m88k-omron
- ;;
magnum | m3230)
basic_machine=mips-mips
os=-sysv
@@ -830,10 +831,10 @@ case $basic_machine in
os=-mint
;;
mips3*-*)
- basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`
+ basic_machine=`echo "$basic_machine" | sed -e 's/mips3/mips64/'`
;;
mips3*)
- basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`-unknown
+ basic_machine=`echo "$basic_machine" | sed -e 's/mips3/mips64/'`-unknown
;;
monitor)
basic_machine=m68k-rom68k
@@ -852,7 +853,7 @@ case $basic_machine in
os=-msdos
;;
ms1-*)
- basic_machine=`echo $basic_machine | sed -e 's/ms1-/mt-/'`
+ basic_machine=`echo "$basic_machine" | sed -e 's/ms1-/mt-/'`
;;
msys)
basic_machine=i686-pc
@@ -894,7 +895,7 @@ case $basic_machine in
basic_machine=v70-nec
os=-sysv
;;
- next | m*-next )
+ next | m*-next)
basic_machine=m68k-next
case $os in
-nextstep* )
@@ -939,6 +940,12 @@ case $basic_machine in
nsr-tandem)
basic_machine=nsr-tandem
;;
+ nsv-tandem)
+ basic_machine=nsv-tandem
+ ;;
+ nsx-tandem)
+ basic_machine=nsx-tandem
+ ;;
op50n-* | op60c-*)
basic_machine=hppa1.1-oki
os=-proelf
@@ -971,7 +978,7 @@ case $basic_machine in
os=-linux
;;
parisc-*)
- basic_machine=hppa-`echo $basic_machine | sed 's/^[^-]*-//'`
+ basic_machine=hppa-`echo "$basic_machine" | sed 's/^[^-]*-//'`
os=-linux
;;
pbd)
@@ -987,7 +994,7 @@ case $basic_machine in
basic_machine=i386-pc
;;
pc98-*)
- basic_machine=i386-`echo $basic_machine | sed 's/^[^-]*-//'`
+ basic_machine=i386-`echo "$basic_machine" | sed 's/^[^-]*-//'`
;;
pentium | p5 | k5 | k6 | nexgen | viac3)
basic_machine=i586-pc
@@ -1002,16 +1009,16 @@ case $basic_machine in
basic_machine=i786-pc
;;
pentium-* | p5-* | k5-* | k6-* | nexgen-* | viac3-*)
- basic_machine=i586-`echo $basic_machine | sed 's/^[^-]*-//'`
+ basic_machine=i586-`echo "$basic_machine" | sed 's/^[^-]*-//'`
;;
pentiumpro-* | p6-* | 6x86-* | athlon-*)
- basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'`
+ basic_machine=i686-`echo "$basic_machine" | sed 's/^[^-]*-//'`
;;
pentiumii-* | pentium2-* | pentiumiii-* | pentium3-*)
- basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'`
+ basic_machine=i686-`echo "$basic_machine" | sed 's/^[^-]*-//'`
;;
pentium4-*)
- basic_machine=i786-`echo $basic_machine | sed 's/^[^-]*-//'`
+ basic_machine=i786-`echo "$basic_machine" | sed 's/^[^-]*-//'`
;;
pn)
basic_machine=pn-gould
@@ -1021,23 +1028,23 @@ case $basic_machine in
ppc | ppcbe) basic_machine=powerpc-unknown
;;
ppc-* | ppcbe-*)
- basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'`
+ basic_machine=powerpc-`echo "$basic_machine" | sed 's/^[^-]*-//'`
;;
- ppcle | powerpclittle | ppc-le | powerpc-little)
+ ppcle | powerpclittle)
basic_machine=powerpcle-unknown
;;
ppcle-* | powerpclittle-*)
- basic_machine=powerpcle-`echo $basic_machine | sed 's/^[^-]*-//'`
+ basic_machine=powerpcle-`echo "$basic_machine" | sed 's/^[^-]*-//'`
;;
ppc64) basic_machine=powerpc64-unknown
;;
- ppc64-*) basic_machine=powerpc64-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ppc64-*) basic_machine=powerpc64-`echo "$basic_machine" | sed 's/^[^-]*-//'`
;;
- ppc64le | powerpc64little | ppc64-le | powerpc64-little)
+ ppc64le | powerpc64little)
basic_machine=powerpc64le-unknown
;;
ppc64le-* | powerpc64little-*)
- basic_machine=powerpc64le-`echo $basic_machine | sed 's/^[^-]*-//'`
+ basic_machine=powerpc64le-`echo "$basic_machine" | sed 's/^[^-]*-//'`
;;
ps2)
basic_machine=i386-ibm
@@ -1091,17 +1098,10 @@ case $basic_machine in
sequent)
basic_machine=i386-sequent
;;
- sh)
- basic_machine=sh-hitachi
- os=-hms
- ;;
sh5el)
basic_machine=sh5le-unknown
;;
- sh64)
- basic_machine=sh64-unknown
- ;;
- sparclite-wrs | simso-wrs)
+ simso-wrs)
basic_machine=sparclite-wrs
os=-vxworks
;;
@@ -1120,7 +1120,7 @@ case $basic_machine in
os=-sysv4
;;
strongarm-* | thumb-*)
- basic_machine=arm-`echo $basic_machine | sed 's/^[^-]*-//'`
+ basic_machine=arm-`echo "$basic_machine" | sed 's/^[^-]*-//'`
;;
sun2)
basic_machine=m68000-sun
@@ -1242,6 +1242,9 @@ case $basic_machine in
basic_machine=hppa1.1-winbond
os=-proelf
;;
+ x64)
+ basic_machine=x86_64-pc
+ ;;
xbox)
basic_machine=i686-pc
os=-mingw32
@@ -1250,20 +1253,12 @@ case $basic_machine in
basic_machine=xps100-honeywell
;;
xscale-* | xscalee[bl]-*)
- basic_machine=`echo $basic_machine | sed 's/^xscale/arm/'`
+ basic_machine=`echo "$basic_machine" | sed 's/^xscale/arm/'`
;;
ymp)
basic_machine=ymp-cray
os=-unicos
;;
- z8k-*-coff)
- basic_machine=z8k-unknown
- os=-sim
- ;;
- z80-*-coff)
- basic_machine=z80-unknown
- os=-sim
- ;;
none)
basic_machine=none-none
os=-none
@@ -1292,10 +1287,6 @@ case $basic_machine in
vax)
basic_machine=vax-dec
;;
- pdp10)
- # there are many clones, so DEC is not a safe bet
- basic_machine=pdp10-unknown
- ;;
pdp11)
basic_machine=pdp11-dec
;;
@@ -1305,9 +1296,6 @@ case $basic_machine in
sh[1234] | sh[24]a | sh[24]aeb | sh[34]eb | sh[1234]le | sh[23]ele)
basic_machine=sh-unknown
;;
- sparc | sparcv8 | sparcv9 | sparcv9b | sparcv9v)
- basic_machine=sparc-sun
- ;;
cydra)
basic_machine=cydra-cydrome
;;
@@ -1327,7 +1315,7 @@ case $basic_machine in
# Make sure to match an already-canonicalized machine name.
;;
*)
- echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2
+ echo Invalid configuration \`"$1"\': machine \`"$basic_machine"\' not recognized 1>&2
exit 1
;;
esac
@@ -1335,10 +1323,10 @@ esac
# Here we canonicalize certain aliases for manufacturers.
case $basic_machine in
*-digital*)
- basic_machine=`echo $basic_machine | sed 's/digital.*/dec/'`
+ basic_machine=`echo "$basic_machine" | sed 's/digital.*/dec/'`
;;
*-commodore*)
- basic_machine=`echo $basic_machine | sed 's/commodore.*/cbm/'`
+ basic_machine=`echo "$basic_machine" | sed 's/commodore.*/cbm/'`
;;
*)
;;
@@ -1349,8 +1337,8 @@ esac
if [ x"$os" != x"" ]
then
case $os in
- # First match some system type aliases
- # that might get confused with valid system types.
+ # First match some system type aliases that might get confused
+ # with valid system types.
# -solaris* is a basic system type, with this one exception.
-auroraux)
os=-auroraux
@@ -1361,18 +1349,19 @@ case $os in
-solaris)
os=-solaris2
;;
- -svr4*)
- os=-sysv4
- ;;
-unixware*)
os=-sysv4.2uw
;;
-gnu/linux*)
os=`echo $os | sed -e 's|gnu/linux|linux-gnu|'`
;;
- # First accept the basic system types.
+ # es1800 is here to avoid being matched by es* (a different OS)
+ -es1800*)
+ os=-ose
+ ;;
+ # Now accept the basic system types.
# The portable systems comes first.
- # Each alternative MUST END IN A *, to match a version number.
+ # Each alternative MUST end in a * to match a version number.
# -sysv* is not here because it comes later, after sysvr4.
-gnu* | -bsd* | -mach* | -minix* | -genix* | -ultrix* | -irix* \
| -*vms* | -sco* | -esix* | -isc* | -aix* | -cnk* | -sunos | -sunos[34]*\
@@ -1382,24 +1371,26 @@ case $os in
| -aos* | -aros* | -cloudabi* | -sortix* \
| -nindy* | -vxsim* | -vxworks* | -ebmon* | -hms* | -mvs* \
| -clix* | -riscos* | -uniplus* | -iris* | -rtu* | -xenix* \
- | -hiux* | -386bsd* | -knetbsd* | -mirbsd* | -netbsd* \
- | -bitrig* | -openbsd* | -solidbsd* \
+ | -hiux* | -knetbsd* | -mirbsd* | -netbsd* \
+ | -bitrig* | -openbsd* | -solidbsd* | -libertybsd* \
| -ekkobsd* | -kfreebsd* | -freebsd* | -riscix* | -lynxos* \
| -bosx* | -nextstep* | -cxux* | -aout* | -elf* | -oabi* \
| -ptx* | -coff* | -ecoff* | -winnt* | -domain* | -vsta* \
| -udi* | -eabi* | -lites* | -ieee* | -go32* | -aux* \
- | -chorusos* | -chorusrdb* | -cegcc* \
+ | -chorusos* | -chorusrdb* | -cegcc* | -glidix* \
| -cygwin* | -msys* | -pe* | -psos* | -moss* | -proelf* | -rtems* \
- | -mingw32* | -mingw64* | -linux-gnu* | -linux-android* \
+ | -midipix* | -mingw32* | -mingw64* | -linux-gnu* | -linux-android* \
| -linux-newlib* | -linux-musl* | -linux-uclibc* \
| -uxpv* | -beos* | -mpeix* | -udk* | -moxiebox* \
- | -interix* | -uwin* | -mks* | -rhapsody* | -darwin* | -opened* \
+ | -interix* | -uwin* | -mks* | -rhapsody* | -darwin* \
| -openstep* | -oskit* | -conix* | -pw32* | -nonstopux* \
| -storm-chaos* | -tops10* | -tenex* | -tops20* | -its* \
| -os2* | -vos* | -palmos* | -uclinux* | -nucleus* \
- | -morphos* | -superux* | -rtmk* | -rtmk-nova* | -windiss* \
+ | -morphos* | -superux* | -rtmk* | -windiss* \
| -powermax* | -dnix* | -nx6 | -nx7 | -sei* | -dragonfly* \
- | -skyos* | -haiku* | -rdos* | -toppers* | -drops* | -es* | -tirtos*)
+ | -skyos* | -haiku* | -rdos* | -toppers* | -drops* | -es* \
+ | -onefs* | -tirtos* | -phoenix* | -fuchsia* | -redox* | -bme* \
+ | -midnightbsd*)
# Remember, each alternative MUST END IN *, to match a version number.
;;
-qnx*)
@@ -1416,12 +1407,12 @@ case $os in
-nto*)
os=`echo $os | sed -e 's|nto|nto-qnx|'`
;;
- -sim | -es1800* | -hms* | -xray | -os68k* | -none* | -v88r* \
- | -windows* | -osx | -abug | -netware* | -os9* | -beos* | -haiku* \
+ -sim | -xray | -os68k* | -v88r* \
+ | -windows* | -osx | -abug | -netware* | -os9* \
| -macos* | -mpw* | -magic* | -mmixware* | -mon960* | -lnews*)
;;
-mac*)
- os=`echo $os | sed -e 's|mac|macos|'`
+ os=`echo "$os" | sed -e 's|mac|macos|'`
;;
-linux-dietlibc)
os=-linux-dietlibc
@@ -1430,10 +1421,10 @@ case $os in
os=`echo $os | sed -e 's|linux|linux-gnu|'`
;;
-sunos5*)
- os=`echo $os | sed -e 's|sunos5|solaris2|'`
+ os=`echo "$os" | sed -e 's|sunos5|solaris2|'`
;;
-sunos6*)
- os=`echo $os | sed -e 's|sunos6|solaris3|'`
+ os=`echo "$os" | sed -e 's|sunos6|solaris3|'`
;;
-opened*)
os=-openedition
@@ -1444,12 +1435,6 @@ case $os in
-wince*)
os=-wince
;;
- -osfrose*)
- os=-osfrose
- ;;
- -osf*)
- os=-osf
- ;;
-utek*)
os=-bsd
;;
@@ -1474,7 +1459,7 @@ case $os in
-nova*)
os=-rtmk-nova
;;
- -ns2 )
+ -ns2)
os=-nextstep2
;;
-nsk*)
@@ -1496,7 +1481,7 @@ case $os in
-oss*)
os=-sysv3
;;
- -svr4)
+ -svr4*)
os=-sysv4
;;
-svr3)
@@ -1511,32 +1496,38 @@ case $os in
-ose*)
os=-ose
;;
- -es1800*)
- os=-ose
- ;;
- -xenix)
- os=-xenix
- ;;
-*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*)
os=-mint
;;
- -aros*)
- os=-aros
- ;;
-zvmoe)
os=-zvmoe
;;
-dicos*)
os=-dicos
;;
+ -pikeos*)
+ # Until real need of OS specific support for
+ # particular features comes up, bare metal
+ # configurations are quite functional.
+ case $basic_machine in
+ arm*)
+ os=-eabi
+ ;;
+ *)
+ os=-elf
+ ;;
+ esac
+ ;;
-nacl*)
;;
+ -ios)
+ ;;
-none)
;;
*)
# Get rid of the `-' at the beginning of $os.
os=`echo $os | sed 's/[^-]*-//'`
- echo Invalid configuration \`$1\': system \`$os\' not recognized 1>&2
+ echo Invalid configuration \`"$1"\': system \`"$os"\' not recognized 1>&2
exit 1
;;
esac
@@ -1626,12 +1617,12 @@ case $basic_machine in
sparc-* | *-sun)
os=-sunos4.1.1
;;
+ pru-*)
+ os=-elf
+ ;;
*-be)
os=-beos
;;
- *-haiku)
- os=-haiku
- ;;
*-ibm)
os=-aix
;;
@@ -1671,7 +1662,7 @@ case $basic_machine in
m88k-omron*)
os=-luna
;;
- *-next )
+ *-next)
os=-nextstep
;;
*-sequent)
@@ -1686,9 +1677,6 @@ case $basic_machine in
i370-*)
os=-mvs
;;
- *-next)
- os=-nextstep3
- ;;
*-gould)
os=-sysv
;;
@@ -1798,15 +1786,15 @@ case $basic_machine in
vendor=stratus
;;
esac
- basic_machine=`echo $basic_machine | sed "s/unknown/$vendor/"`
+ basic_machine=`echo "$basic_machine" | sed "s/unknown/$vendor/"`
;;
esac
-echo $basic_machine$os
+echo "$basic_machine$os"
exit
# Local variables:
-# eval: (add-hook 'write-file-hooks 'time-stamp)
+# eval: (add-hook 'write-file-functions 'time-stamp)
# time-stamp-start: "timestamp='"
# time-stamp-format: "%:y-%02m-%02d"
# time-stamp-end: "'"
=====================================
configure.ac
=====================================
@@ -1,4 +1,4 @@
-AC_INIT(biobambam2,2.0.147,[germant at miltenyibiotec.de],[biobambam2],[https://gitlab.com/german.tischler/biobambam2])
+AC_INIT(biobambam2,2.0.152,[germant at miltenyibiotec.de],[biobambam2],[https://gitlab.com/german.tischler/biobambam2])
AC_CANONICAL_SYSTEM
AC_PROG_LIBTOOL
@@ -165,7 +165,7 @@ if test ! -z "${with_libmaus2}" ; then
fi
fi
-PKG_CHECK_MODULES([libmaus2],[libmaus2 >= 2.0.683])
+PKG_CHECK_MODULES([libmaus2],[libmaus2 >= 2.0.694])
if test ! -z "${with_libmaus2}" ; then
if test ! -z "${PKGCONFIGPATHSAVE}" ; then
@@ -300,7 +300,7 @@ if test "${have_libmaus2_irods}" = "yes" ; then
fi
fi
- PKG_CHECK_MODULES([libmaus2irods],[libmaus2irods >= 2.0.683])
+ PKG_CHECK_MODULES([libmaus2irods],[libmaus2irods >= 2.0.694])
LIBMAUS2IRODSCPPFLAGS="${libmaus2irods_CFLAGS}"
LIBMAUS2IRODSLIBS="${libmaus2irods_LIBS}"
@@ -463,7 +463,7 @@ AC_ARG_ENABLE(install_uncommon,
AS_HELP_STRING([--enable-install-uncommon],[enable installation of some uncommon programs (default no)]),
[install_uncommon=${enableval}],[install_uncommon=no])
-UNCOMMON="bamfilter bamfixmatecoordinates bamfixmatecoordinatesnamesorted bamtoname bamdisthist fastabgzfextract bamheap bamfrontback bamrandomtag bamheap2 bamheap3 bamtagconversion fastqtobampar bambisect vcffilterinfo vcfpatchcontigprepend vcfconcat vcfsort filtergtf bamconsensus"
+UNCOMMON="bamfilter bamfixmatecoordinates bamfixmatecoordinatesnamesorted bamtoname bamdisthist fastabgzfextract bamheap bamfrontback bamrandomtag bamheap2 bamheap3 bamtagconversion fastqtobampar bambisect vcffilterinfo vcfpatchcontigprepend vcfconcat vcfsort filtergtf bamconsensus vcfreplacecontigs"
UNCOMMONINSTALLED=
UNCOMMONUNINSTALLED=
if test "${install_uncommon}" = "yes" ; then
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+biobambam2 (2.0.152+dfsg-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+
+ -- Steffen Moeller <moeller at debian.org> Fri, 24 Jan 2020 12:37:00 +0100
+
biobambam2 (2.0.147+dfsg-1) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -5,7 +5,7 @@ Section: science
Priority: optional
Build-Depends: debhelper-compat (= 12),
pkg-config,
- libmaus2-dev (>= 2.0.284)
+ libmaus2-dev
Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/med-team/biobambam2
Vcs-Git: https://salsa.debian.org/med-team/biobambam2.git
=====================================
src/Makefile.am
=====================================
@@ -138,6 +138,7 @@ EXTRA_PROGRAMS = blastnxmltobam \
vcfpatchcontigprepend \
vcfconcat \
vcfsort \
+ vcfreplacecontigs \
filtergtf
populaterefcache_SOURCES = programs/populaterefcache.cpp biobambam2/Licensing.cpp
@@ -600,6 +601,11 @@ vcfsort_LDADD = ${LIBMAUS2LIBS}
vcfsort_LDFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS} ${LIBMAUS2LDFLAGS} ${AM_LDFLAGS}
vcfsort_CPPFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS}
+vcfreplacecontigs_SOURCES = programs/vcfreplacecontigs.cpp biobambam2/Licensing.cpp
+vcfreplacecontigs_LDADD = ${LIBMAUS2LIBS}
+vcfreplacecontigs_LDFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS} ${LIBMAUS2LDFLAGS} ${AM_LDFLAGS}
+vcfreplacecontigs_CPPFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS}
+
bamfiltereofblocks_SOURCES = programs/bamfiltereofblocks.cpp biobambam2/Licensing.cpp biobambam2/RunEOFFilter.cpp
bamfiltereofblocks_LDADD = ${LIBMAUS2LIBS}
bamfiltereofblocks_LDFLAGS = ${AM_CPPFLAGS} ${LIBMAUS2CPPFLAGS} ${LIBMAUS2LDFLAGS} ${AM_LDFLAGS}
=====================================
src/programs/bamauxmerge2.cpp
=====================================
@@ -47,6 +47,7 @@
#include <libmaus2/util/LELoad.hpp>
#include <libmaus2/bambam/ProgramHeaderLineSet.hpp>
#include <libmaus2/fastx/FastAReader.hpp>
+#include <libmaus2/bambam/StrCmpNum.hpp>
#include <biobambam2/BamBamConfig.hpp>
#include <biobambam2/Licensing.hpp>
=====================================
src/programs/bamconsensus.cpp
=====================================
@@ -1854,7 +1854,6 @@ std::vector<ConsensusPart> handleConsensus(
}
#endif
-
// get set of branch points
std::set<BranchPoint> SBP;
for ( uint64_t i = 0; i < VBL.size(); ++i )
@@ -1873,17 +1872,22 @@ std::vector<ConsensusPart> handleConsensus(
BranchPoint const & from = cur.from;
BranchPoint const & to = cur.to;
+ // get from id in branch point vector
uint64_t const fromid = std::lower_bound(VBP.begin(),VBP.begin()+VBP.size(),from) - VBP.begin();
assert ( fromid < VBP.size() && VBP[fromid] == from );
+ // get to id in branch point vector
uint64_t const toid = std::lower_bound(VBP.begin(),VBP.begin()+VBP.size(),to) - VBP.begin();
+ //
assert ( toid < VBP.size() && VBP[toid] == to );
+ // store link (1 based)
edgeMap[fromid+1].push_back(toid+1);
}
std::vector< std::vector<uint64_t> > Vcomp;
std::map<uint64_t,uint64_t> Vcompmap;
+ // compute connected components
{
std::set<uint64_t> unseen;
std::map<uint64_t,std::vector<uint64_t> > redgeMap;
@@ -1900,7 +1904,6 @@ std::vector<ConsensusPart> handleConsensus(
}
}
-
while ( unseen.size() )
{
#if 0
@@ -1945,9 +1948,11 @@ std::vector<ConsensusPart> handleConsensus(
std::vector<uint64_t> const V(component.begin(),component.end());
+ // set branch point id to component map
for ( uint64_t i = 0; i < V.size(); ++i )
Vcompmap[V[i]] = Vcomp.size();
+ // push connected component
Vcomp.push_back(V);
#if 0
@@ -1959,6 +1964,7 @@ std::vector<ConsensusPart> handleConsensus(
}
}
+ // consider connected components
for ( uint64_t z = 0; z < Vcomp.size(); ++z )
{
std::vector<uint64_t> const & V = Vcomp[z];
@@ -1968,13 +1974,16 @@ std::vector<ConsensusPart> handleConsensus(
int64_t maxx = -1;
int64_t maxu = -1;
+ // iterate over branch points in component
for ( uint64_t y = 0; y < V.size(); ++y )
{
assert ( V[y] > 0 );
+ // get branch point
BranchPoint const & BP = VBP[V[y]-1];
typedef std::vector<BranchLink>::const_iterator it;
+ // get branch links originating from BP
std::pair<it,it> const P = std::equal_range(
VBL.begin(),
VBL.end(),
@@ -1982,9 +1991,12 @@ std::vector<ConsensusPart> handleConsensus(
BranchLinkFromComparator()
);
+ // iterate over branch links
for ( it x = P.first; x != P.second; ++x )
{
+ // get link
BranchLink const & BL = *x;
+ // get kmer links
KmerLink const * KL_A = AKLBL.begin() + BL.link_start;
KmerLink const * KL_E = AKLBL.begin() + BL.link_end;
@@ -1993,8 +2005,10 @@ std::vector<ConsensusPart> handleConsensus(
// std::cerr << BL << std::endl;
+ // iterate over kmer links on branch link
for ( KmerLink const * KL_C = KL_A; KL_C != KL_E; ++KL_C )
{
+ // get frequency of from and to
int64_t const fromfreq = KL_C->fromfreq;
int64_t const tofreq = KL_C->tofreq;
@@ -2021,10 +2035,12 @@ std::vector<ConsensusPart> handleConsensus(
assert ( maxfreq > 0 );
+ // get branch point carying maximum frequency link
BranchPoint const & BP = VBP[V[maxy]-1];
typedef std::vector<BranchLink>::const_iterator it;
+ // get vector of links originating from BP
std::pair<it,it> const P = std::equal_range(
VBL.begin(),
VBL.end(),
@@ -2048,8 +2064,10 @@ std::vector<ConsensusPart> handleConsensus(
BranchLink curBL = P.first[maxx];
VBLmax.push_back(curBL);
+ // follow backward links from curBL
while ( true )
{
+ // look for links
std::pair<it,it> const LP =
std::equal_range(
VBLto.begin(),
@@ -2058,8 +2076,10 @@ std::vector<ConsensusPart> handleConsensus(
BranchLinkToComparator()
);
+ // if any
if ( LP.second-LP.first )
{
+ // look for maximum weight
double weight = -std::numeric_limits<double>::max();
int64_t maxi = -1;
for ( int64_t i = 0; i < LP.second-LP.first; ++i )
@@ -2079,6 +2099,7 @@ std::vector<ConsensusPart> handleConsensus(
}
}
+ // reverse path (we were going backward)
std::reverse(VBLmax.begin(),VBLmax.end());
curBL = P.first[maxx];
@@ -2086,8 +2107,10 @@ std::vector<ConsensusPart> handleConsensus(
std::vector<BranchLink> VBLfrom(VBL);
std::sort(VBLfrom.begin(),VBLfrom.end(),BranchLinkFromComparator());
+ // follow forward
while ( true )
{
+ // look for extensions
std::pair<it,it> const LP =
std::equal_range(
VBLfrom.begin(),
@@ -2096,8 +2119,10 @@ std::vector<ConsensusPart> handleConsensus(
BranchLinkFromComparator()
);
+ // if any
if ( LP.second-LP.first )
{
+ // look for maximum weight
double weight = -std::numeric_limits<double>::max();
int64_t maxi = -1;
for ( int64_t i = 0; i < LP.second-LP.first; ++i )
@@ -2123,6 +2148,7 @@ std::vector<ConsensusPart> handleConsensus(
std::cerr << "full path" << std::endl;
#endif
+ // decode kmer path
std::ostringstream fullpathstr;
if ( VBLmax.size() )
{
=====================================
src/programs/bamfeaturecount.cpp
=====================================
@@ -137,6 +137,8 @@ int bamfeaturecount(libmaus2::util::ArgInfo const & arginfo)
libmaus2::gtf::GTFData::unique_ptr_type pGTF(libmaus2::gtf::GTFData::obtain(annofn,verbose));
libmaus2::gtf::GTFData const & gtfdata = *pGTF;
+ // gtfdata.print(std::cerr);
+
if ( exportcdna )
{
if ( !arginfo.hasArg("reference") )
@@ -651,6 +653,10 @@ int bamfeaturecount(libmaus2::util::ArgInfo const & arginfo)
}
#endif
}
+ else
+ {
+ // std::cerr << "[W] no GTF data found for " << algn.formatAlignment(bamheader) << std::endl;
+ }
}
#if 0
@@ -672,7 +678,6 @@ int bamfeaturecount(libmaus2::util::ArgInfo const & arginfo)
{
-
libmaus2::autoarray::AutoArray<libmaus2::gtf::ExonInfo> AEI(gtfdata.Aexon.size());
libmaus2::sorting::SerialisingSortingBufferedOutputFileArray<libmaus2::gtf::ExonInterval>::merger_ptr_type merger(
@@ -695,9 +700,10 @@ int bamfeaturecount(libmaus2::util::ArgInfo const & arginfo)
uint64_t uncovered;
uint64_t basecover;
uint64_t total;
+ uint64_t maxdepth;
DepthCallback()
- : uncovered(0), basecover(0), total(0) {}
+ : uncovered(0), basecover(0), total(0), maxdepth(0) {}
void operator()(uint64_t const from, uint64_t const to, uint64_t const depth)
{
@@ -705,6 +711,9 @@ int bamfeaturecount(libmaus2::util::ArgInfo const & arginfo)
uint64_t const l = to-from;
+ if ( depth > maxdepth )
+ maxdepth = depth;
+
if ( depth )
{
basecover += l * depth;
@@ -841,13 +850,14 @@ int bamfeaturecount(libmaus2::util::ArgInfo const & arginfo)
info.unique.uncovered += DC.uncovered;
info.unique.basecount += DC.basecover;
info.unique.total += DC.total;
+ info.unique.maxdepth = std::max(info.unique.maxdepth,DC.maxdepth);
}
else
{
info.ambig.uncovered += DC.uncovered;
info.ambig.basecount += DC.basecover;
info.ambig.total += DC.total;
-
+ info.ambig.maxdepth = std::max(info.ambig.maxdepth,DC.maxdepth);
}
}
@@ -902,8 +912,7 @@ int bamfeaturecount(libmaus2::util::ArgInfo const & arginfo)
char const * name = gtfdata.Aid.begin() + G.name_offset;
uint64_t o = 0;
- std::string const refidname = bamheader.getRefIDName(G.chr_id);
-
+ std::string const refidname = gtfdata.Vchr[G.chr_id]; //bamheader.getRefIDName(G.chr_id);
for ( uint64_t ti = G.start; ti < G.end; ++ti )
if (
=====================================
src/programs/bamfilterk.cpp
=====================================
@@ -451,13 +451,14 @@ int bamfilterk(libmaus2::util::ArgInfo const & arginfo)
void operator()(uint64_t const kmer, uint64_t const pos, bool const z)
{
+ //std::cerr << "kmer " << kmer << " seqid " << seqid << " pos " << pos << " z " << z << std::endl;
AK.push(o_AK,KMer(kmer,seqid,pos,z));
}
};
Callback CB(i,AK,o_AK);
- KB.kmerCallbackPos(
+ KB.kmerCallbackPosFR(
Vref[i].c_str(),
Vref[i].size(),
CB,
=====================================
src/programs/bamtofastq.1
=====================================
@@ -204,6 +204,10 @@ The suffixes k, m, g, K, M and G can be used to denote that the argument is
to be multiplied by 1024, 1024^2, 1024^3, 1000, 1000^2 or 1000^3
respectively.
.PP
+.B cols=<>:
+If set to an unsigned number then wrap the sequence and quality lines at
+this number of columns. By default no wrapping is performed.
+.PP
.B splitprefix=<bamtofastq_split>:
file prefix if split>0 and collate=0.
.PP
=====================================
src/programs/bamtofastq.cpp
=====================================
@@ -229,6 +229,11 @@ static uint64_t getDefaultMaxOutput()
return std::numeric_limits<uint64_t>::max();
}
+static uint64_t getDefaultCols()
+{
+ return 0;
+}
+
template<bamtofastq_conversion_type conversion_type>
void bamtofastqNonCollating(libmaus2::util::ArgInfo const & arginfo, libmaus2::bambam::BamAlignmentDecoder & bamdec)
{
@@ -239,6 +244,7 @@ void bamtofastqNonCollating(libmaus2::util::ArgInfo const & arginfo, libmaus2::b
bool const gz = arginfo.getValue<int>("gz",0);
uint64_t const split = arginfo.getValueUnsignedNumeric("split",getDefaultSplit());
uint64_t const maxoutput = arginfo.getValueUnsignedNumeric("maxoutput",getDefaultMaxOutput());
+ uint64_t const cols = arginfo.getValueUnsignedNumeric("cols",getDefaultCols());
std::string splitprefix = arginfo.getUnparsedValue("splitprefix",getDefaultSplitPrefix());
int const level = libmaus2::bambam::BamBlockWriterBaseFactory::checkCompressionLevel(arginfo.getValue<int>("level",Z_DEFAULT_COMPRESSION));
uint32_t const excludeflags = libmaus2::bambam::BamFlagBase::stringToFlags(arginfo.getValue<std::string>("exclude","SECONDARY,SUPPLEMENTARY"));
@@ -256,6 +262,14 @@ void bamtofastqNonCollating(libmaus2::util::ArgInfo const & arginfo, libmaus2::b
std::vector<std::string> const Vtags = parseTags(s_auxtags);
libmaus2::bambam::BamAuxFilterVector auxtags(Vtags);
+ if ( cols%2 == 1 )
+ {
+ libmaus2::exception::LibMausException lme;
+ lme.getStream() << "[E] uneven numbers (" << cols << ") for cols are not supported" << std::endl;
+ lme.finish();
+ throw lme;
+ }
+
if ( split )
{
uint64_t const mult = getSplitMultiplier<conversion_type>();
@@ -298,19 +312,19 @@ void bamtofastqNonCollating(libmaus2::util::ArgInfo const & arginfo, libmaus2::b
switch ( conversion_type )
{
case bamtofastq_conversion_type_fastq:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQ(algn.D.begin(),T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQ(algn.D.begin(),T,cols);
break;
case bamtofastq_conversion_type_fastq_casava18:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQCasava18(algn.D.begin(),algn.blocksize,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQCasava18(algn.D.begin(),algn.blocksize,T,cols);
break;
case bamtofastq_conversion_type_fasta:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastA(algn.D.begin(),T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastA(algn.D.begin(),T,cols);
break;
case bamtofastq_conversion_type_fastq_try_oq:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQTryOQ(algn.D.begin(),algn.blocksize,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQTryOQ(algn.D.begin(),algn.blocksize,T,cols);
break;
case bamtofastq_conversion_type_fastq_aux:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQAux(algn.D.begin(),algn.blocksize,auxtags,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQAux(algn.D.begin(),algn.blocksize,auxtags,T,cols);
break;
}
@@ -437,6 +451,15 @@ void bamtofastqCollating(
CollateCombs combs;
bool const outputperreadgroup = arginfo.getValue<unsigned int>("outputperreadgroup",getDefaultOutputPerReadgroup());
+ uint64_t const cols = arginfo.getValueUnsignedNumeric("cols",getDefaultCols());
+
+ if ( cols%2 == 1 )
+ {
+ libmaus2::exception::LibMausException lme;
+ lme.getStream() << "[E] uneven numbers (" << cols << ") for cols are not supported" << std::endl;
+ lme.finish();
+ throw lme;
+ }
std::string const s_auxtags = arginfo.getUnparsedValue("tags",getDefaultTags());
std::vector<std::string> const Vtags = parseTags(s_auxtags);
@@ -611,19 +634,19 @@ void bamtofastqCollating(
switch ( conversion_type )
{
case bamtofastq_conversion_type_fasta:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastA(ob->Da,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastA(ob->Da,T,cols);
break;
case bamtofastq_conversion_type_fastq:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQ(ob->Da,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQ(ob->Da,T,cols);
break;
case bamtofastq_conversion_type_fastq_casava18:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQCasava18(ob->Da,ob->blocksizea,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQCasava18(ob->Da,ob->blocksizea,T,cols);
break;
case bamtofastq_conversion_type_fastq_try_oq:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQTryOQ(ob->Da,ob->blocksizea,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQTryOQ(ob->Da,ob->blocksizea,T,cols);
break;
case bamtofastq_conversion_type_fastq_aux:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQAux(ob->Da,ob->blocksizea,auxtags,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQAux(ob->Da,ob->blocksizea,auxtags,T,cols);
break;
}
@@ -634,19 +657,19 @@ void bamtofastqCollating(
switch ( conversion_type )
{
case bamtofastq_conversion_type_fasta:
- lb = libmaus2::bambam::BamAlignmentDecoderBase::putFastA(ob->Db,T);
+ lb = libmaus2::bambam::BamAlignmentDecoderBase::putFastA(ob->Db,T,cols);
break;
case bamtofastq_conversion_type_fastq:
- lb = libmaus2::bambam::BamAlignmentDecoderBase::putFastQ(ob->Db,T);
+ lb = libmaus2::bambam::BamAlignmentDecoderBase::putFastQ(ob->Db,T,cols);
break;
case bamtofastq_conversion_type_fastq_casava18:
- lb = libmaus2::bambam::BamAlignmentDecoderBase::putFastQCasava18(ob->Db,ob->blocksizeb,T);
+ lb = libmaus2::bambam::BamAlignmentDecoderBase::putFastQCasava18(ob->Db,ob->blocksizeb,T,cols);
break;
case bamtofastq_conversion_type_fastq_try_oq:
- lb = libmaus2::bambam::BamAlignmentDecoderBase::putFastQTryOQ(ob->Db,ob->blocksizeb,T);
+ lb = libmaus2::bambam::BamAlignmentDecoderBase::putFastQTryOQ(ob->Db,ob->blocksizeb,T,cols);
break;
case bamtofastq_conversion_type_fastq_aux:
- lb = libmaus2::bambam::BamAlignmentDecoderBase::putFastQAux(ob->Db,ob->blocksizeb,auxtags,T);
+ lb = libmaus2::bambam::BamAlignmentDecoderBase::putFastQAux(ob->Db,ob->blocksizeb,auxtags,T,cols);
break;
}
@@ -663,19 +686,19 @@ void bamtofastqCollating(
switch ( conversion_type )
{
case bamtofastq_conversion_type_fasta:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastA(ob->Da,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastA(ob->Da,T,cols);
break;
case bamtofastq_conversion_type_fastq:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQ(ob->Da,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQ(ob->Da,T,cols);
break;
case bamtofastq_conversion_type_fastq_casava18:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQCasava18(ob->Da,ob->blocksizea,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQCasava18(ob->Da,ob->blocksizea,T,cols);
break;
case bamtofastq_conversion_type_fastq_try_oq:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQTryOQ(ob->Da,ob->blocksizea,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQTryOQ(ob->Da,ob->blocksizea,T,cols);
break;
case bamtofastq_conversion_type_fastq_aux:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQAux(ob->Da,ob->blocksizea,auxtags,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQAux(ob->Da,ob->blocksizea,auxtags,T,cols);
break;
}
@@ -692,19 +715,19 @@ void bamtofastqCollating(
switch ( conversion_type )
{
case bamtofastq_conversion_type_fasta:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastA(ob->Da,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastA(ob->Da,T,cols);
break;
case bamtofastq_conversion_type_fastq:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQ(ob->Da,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQ(ob->Da,T,cols);
break;
case bamtofastq_conversion_type_fastq_casava18:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQCasava18(ob->Da,ob->blocksizea,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQCasava18(ob->Da,ob->blocksizea,T,cols);
break;
case bamtofastq_conversion_type_fastq_try_oq:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQTryOQ(ob->Da,ob->blocksizea,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQTryOQ(ob->Da,ob->blocksizea,T,cols);
break;
case bamtofastq_conversion_type_fastq_aux:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQAux(ob->Da,ob->blocksizea,auxtags,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQAux(ob->Da,ob->blocksizea,auxtags,T,cols);
break;
}
@@ -721,19 +744,19 @@ void bamtofastqCollating(
switch ( conversion_type )
{
case bamtofastq_conversion_type_fasta:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastA(ob->Da,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastA(ob->Da,T,cols);
break;
case bamtofastq_conversion_type_fastq:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQ(ob->Da,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQ(ob->Da,T,cols);
break;
case bamtofastq_conversion_type_fastq_casava18:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQCasava18(ob->Da,ob->blocksizea,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQCasava18(ob->Da,ob->blocksizea,T,cols);
break;
case bamtofastq_conversion_type_fastq_try_oq:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQTryOQ(ob->Da,ob->blocksizea,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQTryOQ(ob->Da,ob->blocksizea,T,cols);
break;
case bamtofastq_conversion_type_fastq_aux:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQAux(ob->Da,ob->blocksizea,auxtags,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQAux(ob->Da,ob->blocksizea,auxtags,T,cols);
break;
}
@@ -796,19 +819,19 @@ void bamtofastqCollating(
switch ( conversion_type )
{
case bamtofastq_conversion_type_fasta:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastA(ob->Da,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastA(ob->Da,T,cols);
break;
case bamtofastq_conversion_type_fastq:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQ(ob->Da,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQ(ob->Da,T,cols);
break;
case bamtofastq_conversion_type_fastq_casava18:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQCasava18(ob->Da,ob->blocksizea,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQCasava18(ob->Da,ob->blocksizea,T,cols);
break;
case bamtofastq_conversion_type_fastq_try_oq:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQTryOQ(ob->Da,ob->blocksizea,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQTryOQ(ob->Da,ob->blocksizea,T,cols);
break;
case bamtofastq_conversion_type_fastq_aux:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQAux(ob->Da,ob->blocksizea,auxtags,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQAux(ob->Da,ob->blocksizea,auxtags,T,cols);
break;
}
OFS.Fout.write(reinterpret_cast<char const *>(T.begin()),la);
@@ -817,19 +840,19 @@ void bamtofastqCollating(
switch ( conversion_type )
{
case bamtofastq_conversion_type_fasta:
- lb = libmaus2::bambam::BamAlignmentDecoderBase::putFastA(ob->Db,T);
+ lb = libmaus2::bambam::BamAlignmentDecoderBase::putFastA(ob->Db,T,cols);
break;
case bamtofastq_conversion_type_fastq:
- lb = libmaus2::bambam::BamAlignmentDecoderBase::putFastQ(ob->Db,T);
+ lb = libmaus2::bambam::BamAlignmentDecoderBase::putFastQ(ob->Db,T,cols);
break;
case bamtofastq_conversion_type_fastq_casava18:
- lb = libmaus2::bambam::BamAlignmentDecoderBase::putFastQCasava18(ob->Db,ob->blocksizeb,T);
+ lb = libmaus2::bambam::BamAlignmentDecoderBase::putFastQCasava18(ob->Db,ob->blocksizeb,T,cols);
break;
case bamtofastq_conversion_type_fastq_try_oq:
- lb = libmaus2::bambam::BamAlignmentDecoderBase::putFastQTryOQ(ob->Db,ob->blocksizeb,T);
+ lb = libmaus2::bambam::BamAlignmentDecoderBase::putFastQTryOQ(ob->Db,ob->blocksizeb,T,cols);
break;
case bamtofastq_conversion_type_fastq_aux:
- lb = libmaus2::bambam::BamAlignmentDecoderBase::putFastQAux(ob->Db,ob->blocksizeb,auxtags,T);
+ lb = libmaus2::bambam::BamAlignmentDecoderBase::putFastQAux(ob->Db,ob->blocksizeb,auxtags,T,cols);
break;
}
OFS.F2out.write(reinterpret_cast<char const *>(T.begin()),lb);
@@ -844,19 +867,19 @@ void bamtofastqCollating(
switch ( conversion_type )
{
case bamtofastq_conversion_type_fasta:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastA(ob->Da,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastA(ob->Da,T,cols);
break;
case bamtofastq_conversion_type_fastq:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQ(ob->Da,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQ(ob->Da,T,cols);
break;
case bamtofastq_conversion_type_fastq_casava18:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQCasava18(ob->Da,ob->blocksizea,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQCasava18(ob->Da,ob->blocksizea,T,cols);
break;
case bamtofastq_conversion_type_fastq_try_oq:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQTryOQ(ob->Da,ob->blocksizea,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQTryOQ(ob->Da,ob->blocksizea,T,cols);
break;
case bamtofastq_conversion_type_fastq_aux:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQAux(ob->Da,ob->blocksizea,auxtags,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQAux(ob->Da,ob->blocksizea,auxtags,T,cols);
break;
}
OFS.Sout.write(reinterpret_cast<char const *>(T.begin()),la);
@@ -871,19 +894,19 @@ void bamtofastqCollating(
switch ( conversion_type )
{
case bamtofastq_conversion_type_fasta:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastA(ob->Da,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastA(ob->Da,T,cols);
break;
case bamtofastq_conversion_type_fastq:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQ(ob->Da,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQ(ob->Da,T,cols);
break;
case bamtofastq_conversion_type_fastq_casava18:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQCasava18(ob->Da,ob->blocksizea,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQCasava18(ob->Da,ob->blocksizea,T,cols);
break;
case bamtofastq_conversion_type_fastq_try_oq:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQTryOQ(ob->Da,ob->blocksizea,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQTryOQ(ob->Da,ob->blocksizea,T,cols);
break;
case bamtofastq_conversion_type_fastq_aux:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQAux(ob->Da,ob->blocksizea,auxtags,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQAux(ob->Da,ob->blocksizea,auxtags,T,cols);
break;
}
OFS.Oout.write(reinterpret_cast<char const *>(T.begin()),la);
@@ -898,19 +921,19 @@ void bamtofastqCollating(
switch ( conversion_type )
{
case bamtofastq_conversion_type_fasta:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastA(ob->Da,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastA(ob->Da,T,cols);
break;
case bamtofastq_conversion_type_fastq:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQ(ob->Da,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQ(ob->Da,T,cols);
break;
case bamtofastq_conversion_type_fastq_casava18:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQCasava18(ob->Da,ob->blocksizea,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQCasava18(ob->Da,ob->blocksizea,T,cols);
break;
case bamtofastq_conversion_type_fastq_try_oq:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQTryOQ(ob->Da,ob->blocksizea,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQTryOQ(ob->Da,ob->blocksizea,T,cols);
break;
case bamtofastq_conversion_type_fastq_aux:
- la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQAux(ob->Da,ob->blocksizea,auxtags,T);
+ la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQAux(ob->Da,ob->blocksizea,auxtags,T,cols);
break;
}
OFS.O2out.write(reinterpret_cast<char const *>(T.begin()),la);
@@ -1037,6 +1060,15 @@ void bamtofastqCollatingRanking(
CHCBD.disableValidation();
libmaus2::bambam::BamToFastqOutputFileSet OFS(arginfo);
+ uint64_t const cols = arginfo.getValueUnsignedNumeric("cols",getDefaultCols());
+
+ if ( cols%2 == 1 )
+ {
+ libmaus2::exception::LibMausException lme;
+ lme.getStream() << "[E] uneven numbers (" << cols << ") for cols are not supported" << std::endl;
+ lme.finish();
+ throw lme;
+ }
try
{
@@ -1059,9 +1091,9 @@ void bamtofastqCollatingRanking(
{
uint64_t const ranka = libmaus2::bambam::BamAlignmentDecoderBase::getRank(ob->Da,ob->blocksizea);
uint64_t const rankb = libmaus2::bambam::BamAlignmentDecoderBase::getRank(ob->Db,ob->blocksizeb);
- uint64_t const la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQRanks(ob->Da,ranka,rankb,T);
+ uint64_t const la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQRanks(ob->Da,ranka,rankb,T,cols);
OFS.Fout.write(reinterpret_cast<char const *>(T.begin()),la);
- uint64_t lb = libmaus2::bambam::BamAlignmentDecoderBase::putFastQRanks(ob->Db,ranka,rankb,T);
+ uint64_t lb = libmaus2::bambam::BamAlignmentDecoderBase::putFastQRanks(ob->Db,ranka,rankb,T,cols);
OFS.F2out.write(reinterpret_cast<char const *>(T.begin()),lb);
combs.pairs += 1;
@@ -1072,7 +1104,7 @@ void bamtofastqCollatingRanking(
{
uint64_t const ranka = libmaus2::bambam::BamAlignmentDecoderBase::getRank(ob->Da,ob->blocksizea);
- uint64_t la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQRanks(ob->Da,ranka,ranka,T);
+ uint64_t la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQRanks(ob->Da,ranka,ranka,T,cols);
OFS.Sout.write(reinterpret_cast<char const *>(T.begin()),la);
combs.single += 1;
@@ -1083,7 +1115,7 @@ void bamtofastqCollatingRanking(
{
uint64_t const ranka = libmaus2::bambam::BamAlignmentDecoderBase::getRank(ob->Da,ob->blocksizea);
- uint64_t la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQRanks(ob->Da,ranka,ranka,T);
+ uint64_t la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQRanks(ob->Da,ranka,ranka,T,cols);
OFS.Oout.write(reinterpret_cast<char const *>(T.begin()),la);
combs.orphans1 += 1;
@@ -1094,7 +1126,7 @@ void bamtofastqCollatingRanking(
{
uint64_t const ranka = libmaus2::bambam::BamAlignmentDecoderBase::getRank(ob->Da,ob->blocksizea);
- uint64_t la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQRanks(ob->Da,ranka,ranka,T);
+ uint64_t la = libmaus2::bambam::BamAlignmentDecoderBase::putFastQRanks(ob->Da,ranka,ranka,T,cols);
OFS.O2out.write(reinterpret_cast<char const *>(T.begin()),la);
combs.orphans2 += 1;
@@ -1299,6 +1331,7 @@ int main(int argc, char * argv[])
V.push_back ( std::pair<std::string,std::string> ( "outputperreadgroupprefix=<[]>", "prefix added in front of file names if outputperreadgroup=1 (for collate=1 only)" ) );
V.push_back ( std::pair<std::string,std::string> ( std::string("casava18=<[")+libmaus2::util::NumberSerialisation::formatNumber(getDefaultCasava18(),0)+"]>", "restore input taken by c18pe option" ) );
V.push_back ( std::pair<std::string,std::string> ( "maxoutput=<[]>", "output no more than this number of entries (default: no limit, collate=0 only)" ) );
+ V.push_back ( std::pair<std::string,std::string> ( "cols=<[]>", "wrap sequence and quality lines at this number of columns (default: do not wrap, even numbers only)" ) );
::biobambam2::Licensing::printMap(std::cerr,V);
=====================================
src/programs/vcfreplacecontigs.cpp
=====================================
@@ -0,0 +1,188 @@
+/**
+ bambam
+ Copyright (C) 2019 German Tischler
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+**/
+#include <config.h>
+
+#include <libmaus2/vcf/VCFParser.hpp>
+#include <libmaus2/util/ArgInfo.hpp>
+#include <libmaus2/lz/BgzfDeflate.hpp>
+#include <libmaus2/fastx/FastAReader.hpp>
+
+#include <biobambam2/Licensing.hpp>
+
+static int getDefaultVerbose() { return 0; }
+
+int vcfreplacecontigs(libmaus2::util::ArgInfo const & arginfo, std::istream & in, std::ostream & out)
+{
+ //unsigned int const verbose = arginfo.getValue<unsigned int>("verbose",getDefaultVerbose());
+ bool const gz = arginfo.getValue<int>("gz",0);
+
+ libmaus2::lz::BgzfOutputStream::unique_ptr_type pBOS;
+
+ if ( gz )
+ {
+ libmaus2::lz::BgzfOutputStream::unique_ptr_type tBOS(new libmaus2::lz::BgzfOutputStream(out));
+ pBOS = UNIQUE_PTR_MOVE(tBOS);
+ }
+
+ std::ostream & vout = gz ? *pBOS : out;
+
+ libmaus2::vcf::VCFParser vcf(in);
+
+ if ( ! ( 0 < arginfo.getNumRestArgs() ) )
+ {
+ std::cerr << "[E] usage: " << arginfo.progname << " <in.fa> <in.vcf" << std::endl;
+ return EXIT_FAILURE;
+ }
+
+ std::string const fafn = arginfo.getUnparsedRestArg(0);
+ std::vector<libmaus2::bambam::Chromosome> V;
+ std::set<std::string> S;
+ {
+ libmaus2::fastx::FastAReader FA(fafn);
+ libmaus2::fastx::FastAReader::pattern_type pat;
+ while ( FA.getNextPatternUnlocked(pat) )
+ {
+ std::string const name = pat.getShortStringId();
+ V.push_back(libmaus2::bambam::Chromosome(name,pat.spattern.size()));
+ S.insert(name);
+ std::cerr << "[V] pushed " << name << "[" << pat.spattern.size() << "]" << std::endl;
+ }
+ }
+
+ vcf.setChromosomeVector(V);
+ vcf.printText(vout);
+
+
+ std::pair<
+ libmaus2::util::TabEntry<> const *,
+ char const *
+ > P;
+
+ std::pair<
+ std::vector<std::string>,
+ ::libmaus2::trie::LinearHashTrie<char,uint32_t>::shared_ptr_type
+ > const Pcontig = vcf.getContigNamesAndTrie();
+
+ uint64_t line = 0;
+ while ( (P = vcf.readEntry()).first )
+ {
+ if ( P.first->size() )
+ {
+ std::pair<char const *, char const *> const Pchr = P.first->get(0,P.second);
+
+ if ( Pcontig.second->searchCompleteNoFailure(Pchr.first,Pchr.second) != -1 )
+ {
+ char const * a = P.first->get(0,P.second).first;
+ char const * e = P.first->get(P.first->size()-1,P.second).second;
+
+ vout.write(a,e-a);
+ vout.put('\n');
+
+ line += 1;
+
+ if ( line % (1024*1024) == 0 )
+ std::cerr << "[V] " << line << std::endl;
+ }
+ else
+ {
+ libmaus2::exception::LibMausException lme;
+ lme.getStream() << "[E] sequence " << std::string(Pchr.first,Pchr.second) << " does not appear in FastA file provided" << std::endl;
+ lme.finish();
+ throw lme;
+ }
+ }
+ }
+
+ // vcf.unparsedCopy(vout);
+
+ #if 0
+ if ( Vin.size() )
+ {
+ std::pair<bool, char const *> E;
+
+ {
+ libmaus2::aio::InputStreamInstance ISI(Vin[0]);
+ libmaus2::vcf::VCFParser vcf(ISI);
+ vcf.printText(vout);
+ vcf.unparsedCopy(vout);
+ }
+
+ for ( uint64_t j = 1; j < Vin.size(); ++j )
+ {
+ libmaus2::aio::InputStreamInstance ISI(Vin[j]);
+ libmaus2::vcf::VCFParser vcf(ISI);
+ vcf.unparsedCopy(vout);
+ }
+ }
+ #endif
+
+ if ( gz )
+ {
+ pBOS->flush();
+ pBOS->addEOFBlock();
+ pBOS.reset();
+ }
+
+ return EXIT_SUCCESS;
+}
+
+int main(int argc, char * argv[])
+{
+ try
+ {
+ ::libmaus2::util::ArgInfo const arginfo(argc,argv);
+
+ for ( uint64_t i = 0; i < arginfo.restargs.size(); ++i )
+ if (
+ arginfo.restargs[i] == "-v"
+ ||
+ arginfo.restargs[i] == "--version"
+ )
+ {
+ std::cerr << ::biobambam2::Licensing::license();
+ return EXIT_SUCCESS;
+ }
+ else if (
+ arginfo.restargs[i] == "-h"
+ ||
+ arginfo.restargs[i] == "--help"
+ )
+ {
+ std::cerr << ::biobambam2::Licensing::license();
+ std::cerr << std::endl;
+ std::cerr << "Key=Value pairs:" << std::endl;
+ std::cerr << std::endl;
+
+ std::vector< std::pair<std::string,std::string> > V;
+
+ V.push_back ( std::pair<std::string,std::string> ( "verbose=<["+::biobambam2::Licensing::formatNumber(getDefaultVerbose())+"]>", "print progress report (default: 1)" ) );
+
+ ::biobambam2::Licensing::printMap(std::cerr,V);
+
+ std::cerr << std::endl;
+ return EXIT_SUCCESS;
+ }
+
+ return vcfreplacecontigs(arginfo,std::cin,std::cout);
+ }
+ catch(std::exception const & ex)
+ {
+ std::cerr << ex.what() << std::endl;
+ return EXIT_FAILURE;
+ }
+}
View it on GitLab: https://salsa.debian.org/med-team/biobambam2/compare/36661590af842698d671f9e0b1ce6b3a24f417f4...6ebd913d8bd348152d0aa24dbc5585d97bc8ce72
--
View it on GitLab: https://salsa.debian.org/med-team/biobambam2/compare/36661590af842698d671f9e0b1ce6b3a24f417f4...6ebd913d8bd348152d0aa24dbc5585d97bc8ce72
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