[med-svn] r7906 - in trunk/packages/rostlab/libzerg-perl/trunk/debian: . patches
Laszlo Kajan
lkajan-guest at alioth.debian.org
Thu Sep 22 19:56:13 UTC 2011
Author: lkajan-guest
Date: 2011-09-22 19:56:13 +0000 (Thu, 22 Sep 2011)
New Revision: 7906
Added:
trunk/packages/rostlab/libzerg-perl/trunk/debian/patches/
trunk/packages/rostlab/libzerg-perl/trunk/debian/patches/debian-changes-1.0.4-1
trunk/packages/rostlab/libzerg-perl/trunk/debian/patches/new_tokens
trunk/packages/rostlab/libzerg-perl/trunk/debian/patches/series
Modified:
trunk/packages/rostlab/libzerg-perl/trunk/debian/README.source
trunk/packages/rostlab/libzerg-perl/trunk/debian/changelog
Log:
1.0.4-2 read to release: added new tokens from libzerg-1.0.7-2; fixed Report.pm for iterated blast; corrected bug in Report.pm that prevented reporting the last blast result; added the alignments to the structure returned by Report.pm
Modified: trunk/packages/rostlab/libzerg-perl/trunk/debian/README.source
===================================================================
--- trunk/packages/rostlab/libzerg-perl/trunk/debian/README.source 2011-09-22 17:27:22 UTC (rev 7905)
+++ trunk/packages/rostlab/libzerg-perl/trunk/debian/README.source 2011-09-22 19:56:13 UTC (rev 7906)
@@ -2,6 +2,13 @@
-----------------------
patches:
- there are no patches yet
+ debian-changes-1.0.4-1:
+ * automatic patch, captures old Makefiles generated during building
+
+ new_tokens:
+ * added new tokens of libzerg-1.0.7-2 to perl module
+ * extended Report.pm to handle blastpgp (iterated blast) results
+ * corrected bug in Report.pm that prevented reporting the last blast result
+ * added the alignments to the structure returned by Report.pm
# vim:et:ts=2:
Modified: trunk/packages/rostlab/libzerg-perl/trunk/debian/changelog
===================================================================
--- trunk/packages/rostlab/libzerg-perl/trunk/debian/changelog 2011-09-22 17:27:22 UTC (rev 7905)
+++ trunk/packages/rostlab/libzerg-perl/trunk/debian/changelog 2011-09-22 19:56:13 UTC (rev 7906)
@@ -1,5 +1,12 @@
-libzerg-perl (1.0.4-1) UNRELEASED; urgency=low
+libzerg-perl (1.0.4-2) UNRELEASED; urgency=low
+ * added new tokens from libzerg-1.0.7-2
+ * Report.pm now understands blastpgp output, i.e. rounds of iteration
+
+ -- Laszlo Kajan <lkajan at rostlab.org> Thu, 22 Sep 2011 18:43:25 +0200
+
+libzerg-perl (1.0.4-1) unstable; urgency=low
+
* Initial release (Closes: #641799)
-- Laszlo Kajan <lkajan at rostlab.org> Fri, 16 Sep 2011 11:52:32 +0200
Added: trunk/packages/rostlab/libzerg-perl/trunk/debian/patches/debian-changes-1.0.4-1
===================================================================
--- trunk/packages/rostlab/libzerg-perl/trunk/debian/patches/debian-changes-1.0.4-1 (rev 0)
+++ trunk/packages/rostlab/libzerg-perl/trunk/debian/patches/debian-changes-1.0.4-1 2011-09-22 19:56:13 UTC (rev 7906)
@@ -0,0 +1,1584 @@
+Description: Upstream changes introduced in version 1.0.4-1
+ This patch has been created by dpkg-source during the package build.
+ Here's the last changelog entry, hopefully it gives details on why
+ those changes were made:
+ .
+ libzerg-perl (1.0.4-1) UNRELEASED; urgency=low
+ .
+ * Initial release (Closes: #641799)
+ .
+ The person named in the Author field signed this changelog entry.
+Author: Laszlo Kajan <lkajan at rostlab.org>
+Bug-Debian: http://bugs.debian.org/641799
+
+---
+The information above should follow the Patch Tagging Guidelines, please
+checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
+are templates for supplementary fields that you might want to add:
+
+Origin: <vendor|upstream|other>, <url of original patch>
+Bug: <url in upstream bugtracker>
+Bug-Debian: http://bugs.debian.org/<bugnumber>
+Bug-Ubuntu: https://launchpad.net/bugs/<bugnumber>
+Forwarded: <no|not-needed|url proving that it has been forwarded>
+Reviewed-By: <name and email of someone who approved the patch>
+Last-Update: <YYYY-MM-DD>
+
+--- /dev/null
++++ libzerg-perl-1.0.4/Zerg/Makefile.old
+@@ -0,0 +1,950 @@
++# This Makefile is for the Zerg extension to perl.
++#
++# It was generated automatically by MakeMaker version
++# 6.55_02 (Revision: 65502) from the contents of
++# Makefile.PL. Don't edit this file, edit Makefile.PL instead.
++#
++# ANY CHANGES MADE HERE WILL BE LOST!
++#
++# MakeMaker ARGV: (q[INSTALLDIRS=vendor])
++#
++
++# MakeMaker Parameters:
++
++# ABSTRACT_FROM => q[Zerg.pm]
++# AUTHOR => q[Apuã Paquola <apua at iq.usp.br>]
++# BUILD_REQUIRES => { }
++# DEFINE => q[]
++# INC => q[]
++# LIBS => [q[-L/usr/local/lib -lzerg]]
++# NAME => q[Zerg]
++# PREREQ_PM => { }
++# VERSION_FROM => q[Zerg.pm]
++
++# --- MakeMaker post_initialize section:
++
++
++# --- MakeMaker const_config section:
++
++# These definitions are from config.sh (via /usr/lib/perl/5.10/Config.pm).
++# They may have been overridden via Makefile.PL or on the command line.
++AR = ar
++CC = cc
++CCCDLFLAGS = -fPIC
++CCDLFLAGS = -Wl,-E
++DLEXT = so
++DLSRC = dl_dlopen.xs
++EXE_EXT =
++FULL_AR = /usr/bin/ar
++LD = cc
++LDDLFLAGS = -shared -O2 -g -L/usr/local/lib -fstack-protector
++LDFLAGS = -fstack-protector -L/usr/local/lib
++LIBC = /lib/libc-2.11.2.so
++LIB_EXT = .a
++OBJ_EXT = .o
++OSNAME = linux
++OSVERS = 2.6.32-5-amd64
++RANLIB = :
++SITELIBEXP = /usr/local/share/perl/5.10.1
++SITEARCHEXP = /usr/local/lib/perl/5.10.1
++SO = so
++VENDORARCHEXP = /usr/lib/perl5
++VENDORLIBEXP = /usr/share/perl5
++
++
++# --- MakeMaker constants section:
++AR_STATIC_ARGS = cr
++DIRFILESEP = /
++DFSEP = $(DIRFILESEP)
++NAME = Zerg
++NAME_SYM = Zerg
++VERSION = 1.0.4
++VERSION_MACRO = VERSION
++VERSION_SYM = 1_0_4
++DEFINE_VERSION = -D$(VERSION_MACRO)=\"$(VERSION)\"
++XS_VERSION = 1.0.4
++XS_VERSION_MACRO = XS_VERSION
++XS_DEFINE_VERSION = -D$(XS_VERSION_MACRO)=\"$(XS_VERSION)\"
++INST_ARCHLIB = blib/arch
++INST_SCRIPT = blib/script
++INST_BIN = blib/bin
++INST_LIB = blib/lib
++INST_MAN1DIR = blib/man1
++INST_MAN3DIR = blib/man3
++MAN1EXT = 1p
++MAN3EXT = 3pm
++INSTALLDIRS = vendor
++DESTDIR =
++PREFIX = /usr
++PERLPREFIX = $(PREFIX)
++SITEPREFIX = $(PREFIX)/local
++VENDORPREFIX = $(PREFIX)
++INSTALLPRIVLIB = $(PERLPREFIX)/share/perl/5.10
++DESTINSTALLPRIVLIB = $(DESTDIR)$(INSTALLPRIVLIB)
++INSTALLSITELIB = $(SITEPREFIX)/share/perl/5.10.1
++DESTINSTALLSITELIB = $(DESTDIR)$(INSTALLSITELIB)
++INSTALLVENDORLIB = $(VENDORPREFIX)/share/perl5
++DESTINSTALLVENDORLIB = $(DESTDIR)$(INSTALLVENDORLIB)
++INSTALLARCHLIB = $(PERLPREFIX)/lib/perl/5.10
++DESTINSTALLARCHLIB = $(DESTDIR)$(INSTALLARCHLIB)
++INSTALLSITEARCH = $(SITEPREFIX)/lib/perl/5.10.1
++DESTINSTALLSITEARCH = $(DESTDIR)$(INSTALLSITEARCH)
++INSTALLVENDORARCH = $(VENDORPREFIX)/lib/perl5
++DESTINSTALLVENDORARCH = $(DESTDIR)$(INSTALLVENDORARCH)
++INSTALLBIN = $(PERLPREFIX)/bin
++DESTINSTALLBIN = $(DESTDIR)$(INSTALLBIN)
++INSTALLSITEBIN = $(SITEPREFIX)/bin
++DESTINSTALLSITEBIN = $(DESTDIR)$(INSTALLSITEBIN)
++INSTALLVENDORBIN = $(VENDORPREFIX)/bin
++DESTINSTALLVENDORBIN = $(DESTDIR)$(INSTALLVENDORBIN)
++INSTALLSCRIPT = $(PERLPREFIX)/bin
++DESTINSTALLSCRIPT = $(DESTDIR)$(INSTALLSCRIPT)
++INSTALLSITESCRIPT = $(SITEPREFIX)/bin
++DESTINSTALLSITESCRIPT = $(DESTDIR)$(INSTALLSITESCRIPT)
++INSTALLVENDORSCRIPT = $(VENDORPREFIX)/bin
++DESTINSTALLVENDORSCRIPT = $(DESTDIR)$(INSTALLVENDORSCRIPT)
++INSTALLMAN1DIR = $(PERLPREFIX)/share/man/man1
++DESTINSTALLMAN1DIR = $(DESTDIR)$(INSTALLMAN1DIR)
++INSTALLSITEMAN1DIR = $(SITEPREFIX)/man/man1
++DESTINSTALLSITEMAN1DIR = $(DESTDIR)$(INSTALLSITEMAN1DIR)
++INSTALLVENDORMAN1DIR = $(VENDORPREFIX)/share/man/man1
++DESTINSTALLVENDORMAN1DIR = $(DESTDIR)$(INSTALLVENDORMAN1DIR)
++INSTALLMAN3DIR = $(PERLPREFIX)/share/man/man3
++DESTINSTALLMAN3DIR = $(DESTDIR)$(INSTALLMAN3DIR)
++INSTALLSITEMAN3DIR = $(SITEPREFIX)/man/man3
++DESTINSTALLSITEMAN3DIR = $(DESTDIR)$(INSTALLSITEMAN3DIR)
++INSTALLVENDORMAN3DIR = $(VENDORPREFIX)/share/man/man3
++DESTINSTALLVENDORMAN3DIR = $(DESTDIR)$(INSTALLVENDORMAN3DIR)
++PERL_LIB = /usr/share/perl/5.10
++PERL_ARCHLIB = /usr/lib/perl/5.10
++LIBPERL_A = libperl.a
++FIRST_MAKEFILE = Makefile
++MAKEFILE_OLD = Makefile.old
++MAKE_APERL_FILE = Makefile.aperl
++PERLMAINCC = $(CC)
++PERL_INC = /usr/lib/perl/5.10/CORE
++PERL = /usr/bin/perl
++FULLPERL = /usr/bin/perl
++ABSPERL = $(PERL)
++PERLRUN = $(PERL)
++FULLPERLRUN = $(FULLPERL)
++ABSPERLRUN = $(ABSPERL)
++PERLRUNINST = $(PERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)"
++FULLPERLRUNINST = $(FULLPERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)"
++ABSPERLRUNINST = $(ABSPERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)"
++PERL_CORE = 0
++PERM_DIR = 755
++PERM_RW = 644
++PERM_RWX = 755
++
++MAKEMAKER = /usr/share/perl/5.10/ExtUtils/MakeMaker.pm
++MM_VERSION = 6.55_02
++MM_REVISION = 65502
++
++# FULLEXT = Pathname for extension directory (eg Foo/Bar/Oracle).
++# BASEEXT = Basename part of FULLEXT. May be just equal FULLEXT. (eg Oracle)
++# PARENT_NAME = NAME without BASEEXT and no trailing :: (eg Foo::Bar)
++# DLBASE = Basename part of dynamic library. May be just equal BASEEXT.
++MAKE = make
++FULLEXT = Zerg
++BASEEXT = Zerg
++PARENT_NAME =
++DLBASE = $(BASEEXT)
++VERSION_FROM = Zerg.pm
++INC =
++DEFINE =
++OBJECT = $(BASEEXT)$(OBJ_EXT)
++LDFROM = $(OBJECT)
++LINKTYPE = dynamic
++BOOTDEP =
++
++# Handy lists of source code files:
++XS_FILES = Zerg.xs
++C_FILES = Zerg.c
++O_FILES = Zerg.o
++H_FILES =
++MAN1PODS =
++MAN3PODS = Zerg.pm
++
++# Where is the Config information that we are using/depend on
++CONFIGDEP = $(PERL_ARCHLIB)$(DFSEP)Config.pm $(PERL_INC)$(DFSEP)config.h
++
++# Where to build things
++INST_LIBDIR = $(INST_LIB)
++INST_ARCHLIBDIR = $(INST_ARCHLIB)
++
++INST_AUTODIR = $(INST_LIB)/auto/$(FULLEXT)
++INST_ARCHAUTODIR = $(INST_ARCHLIB)/auto/$(FULLEXT)
++
++INST_STATIC = $(INST_ARCHAUTODIR)/$(BASEEXT)$(LIB_EXT)
++INST_DYNAMIC = $(INST_ARCHAUTODIR)/$(DLBASE).$(DLEXT)
++INST_BOOT = $(INST_ARCHAUTODIR)/$(BASEEXT).bs
++
++# Extra linker info
++EXPORT_LIST =
++PERL_ARCHIVE =
++PERL_ARCHIVE_AFTER =
++
++
++TO_INST_PM = Zerg.pm
++
++PM_TO_BLIB = Zerg.pm \
++ $(INST_LIB)/Zerg.pm
++
++
++# --- MakeMaker platform_constants section:
++MM_Unix_VERSION = 6.55_02
++PERL_MALLOC_DEF = -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc
++
++
++# --- MakeMaker tool_autosplit section:
++# Usage: $(AUTOSPLITFILE) FileToSplit AutoDirToSplitInto
++AUTOSPLITFILE = $(ABSPERLRUN) -e 'use AutoSplit; autosplit($$ARGV[0], $$ARGV[1], 0, 1, 1)' --
++
++
++
++# --- MakeMaker tool_xsubpp section:
++
++XSUBPPDIR = /usr/share/perl/5.10/ExtUtils
++XSUBPP = $(XSUBPPDIR)$(DFSEP)xsubpp
++XSUBPPRUN = $(PERLRUN) $(XSUBPP)
++XSPROTOARG =
++XSUBPPDEPS = /usr/share/perl/5.10/ExtUtils/typemap $(XSUBPP)
++XSUBPPARGS = -typemap /usr/share/perl/5.10/ExtUtils/typemap
++XSUBPP_EXTRA_ARGS =
++
++
++# --- MakeMaker tools_other section:
++SHELL = /bin/sh
++CHMOD = chmod
++CP = cp
++MV = mv
++NOOP = $(TRUE)
++NOECHO = @
++RM_F = rm -f
++RM_RF = rm -rf
++TEST_F = test -f
++TOUCH = touch
++UMASK_NULL = umask 0
++DEV_NULL = > /dev/null 2>&1
++MKPATH = $(ABSPERLRUN) -MExtUtils::Command -e 'mkpath' --
++EQUALIZE_TIMESTAMP = $(ABSPERLRUN) -MExtUtils::Command -e 'eqtime' --
++FALSE = false
++TRUE = true
++ECHO = echo
++ECHO_N = echo -n
++UNINST = 0
++VERBINST = 0
++MOD_INSTALL = $(ABSPERLRUN) -MExtUtils::Install -e 'install([ from_to => {@ARGV}, verbose => '\''$(VERBINST)'\'', uninstall_shadows => '\''$(UNINST)'\'', dir_mode => '\''$(PERM_DIR)'\'' ]);' --
++DOC_INSTALL = $(ABSPERLRUN) -MExtUtils::Command::MM -e 'perllocal_install' --
++UNINSTALL = $(ABSPERLRUN) -MExtUtils::Command::MM -e 'uninstall' --
++WARN_IF_OLD_PACKLIST = $(ABSPERLRUN) -MExtUtils::Command::MM -e 'warn_if_old_packlist' --
++MACROSTART =
++MACROEND =
++USEMAKEFILE = -f
++FIXIN = $(ABSPERLRUN) -MExtUtils::MY -e 'MY->fixin(shift)' --
++
++
++# --- MakeMaker makemakerdflt section:
++makemakerdflt : all
++ $(NOECHO) $(NOOP)
++
++
++# --- MakeMaker dist section:
++TAR = tar
++TARFLAGS = cvf
++ZIP = zip
++ZIPFLAGS = -r
++COMPRESS = gzip --best
++SUFFIX = .gz
++SHAR = shar
++PREOP = $(NOECHO) $(NOOP)
++POSTOP = $(NOECHO) $(NOOP)
++TO_UNIX = $(NOECHO) $(NOOP)
++CI = ci -u
++RCS_LABEL = rcs -Nv$(VERSION_SYM): -q
++DIST_CP = best
++DIST_DEFAULT = tardist
++DISTNAME = Zerg
++DISTVNAME = Zerg-1.0.4
++
++
++# --- MakeMaker macro section:
++
++
++# --- MakeMaker depend section:
++
++
++# --- MakeMaker cflags section:
++
++CCFLAGS = -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
++OPTIMIZE = -O2 -g
++PERLTYPE =
++MPOLLUTE =
++
++
++# --- MakeMaker const_loadlibs section:
++
++# Zerg might depend on some other libraries:
++# See ExtUtils::Liblist for details
++#
++EXTRALIBS = -L/usr/local/lib -lzerg
++LDLOADLIBS = -L/usr/local/lib -lzerg
++BSLOADLIBS =
++
++
++# --- MakeMaker const_cccmd section:
++CCCMD = $(CC) -c $(PASTHRU_INC) $(INC) \
++ $(CCFLAGS) $(OPTIMIZE) \
++ $(PERLTYPE) $(MPOLLUTE) $(DEFINE_VERSION) \
++ $(XS_DEFINE_VERSION)
++
++# --- MakeMaker post_constants section:
++
++
++# --- MakeMaker pasthru section:
++
++PASTHRU = LIBPERL_A="$(LIBPERL_A)"\
++ LINKTYPE="$(LINKTYPE)"\
++ OPTIMIZE="$(OPTIMIZE)"\
++ PREFIX="$(PREFIX)"\
++ PASTHRU_DEFINE="$(PASTHRU_DEFINE)"\
++ PASTHRU_INC="$(PASTHRU_INC)"
++
++
++# --- MakeMaker special_targets section:
++.SUFFIXES : .xs .c .C .cpp .i .s .cxx .cc $(OBJ_EXT)
++
++.PHONY: all config static dynamic test linkext manifest blibdirs clean realclean disttest distdir
++
++
++
++# --- MakeMaker c_o section:
++
++.c.i:
++ cc -E -c $(PASTHRU_INC) $(INC) \
++ $(CCFLAGS) $(OPTIMIZE) \
++ $(PERLTYPE) $(MPOLLUTE) $(DEFINE_VERSION) \
++ $(XS_DEFINE_VERSION) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.c > $*.i
++
++.c.s:
++ $(CCCMD) -S $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.c
++
++.c$(OBJ_EXT):
++ $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.c
++
++.cpp$(OBJ_EXT):
++ $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.cpp
++
++.cxx$(OBJ_EXT):
++ $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.cxx
++
++.cc$(OBJ_EXT):
++ $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.cc
++
++.C$(OBJ_EXT):
++ $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.C
++
++
++# --- MakeMaker xs_c section:
++
++.xs.c:
++ $(XSUBPPRUN) $(XSPROTOARG) $(XSUBPPARGS) $(XSUBPP_EXTRA_ARGS) $*.xs > $*.xsc && $(MV) $*.xsc $*.c
++
++
++# --- MakeMaker xs_o section:
++
++.xs$(OBJ_EXT):
++ $(XSUBPPRUN) $(XSPROTOARG) $(XSUBPPARGS) $*.xs > $*.xsc && $(MV) $*.xsc $*.c
++ $(CCCMD) $(CCCDLFLAGS) "-I$(PERL_INC)" $(PASTHRU_DEFINE) $(DEFINE) $*.c
++
++
++# --- MakeMaker top_targets section:
++all :: pure_all manifypods
++ $(NOECHO) $(NOOP)
++
++
++pure_all :: config pm_to_blib subdirs linkext
++ $(NOECHO) $(NOOP)
++
++subdirs :: $(MYEXTLIB)
++ $(NOECHO) $(NOOP)
++
++config :: $(FIRST_MAKEFILE) blibdirs
++ $(NOECHO) $(NOOP)
++
++help :
++ perldoc ExtUtils::MakeMaker
++
++
++# --- MakeMaker blibdirs section:
++blibdirs : $(INST_LIBDIR)$(DFSEP).exists $(INST_ARCHLIB)$(DFSEP).exists $(INST_AUTODIR)$(DFSEP).exists $(INST_ARCHAUTODIR)$(DFSEP).exists $(INST_BIN)$(DFSEP).exists $(INST_SCRIPT)$(DFSEP).exists $(INST_MAN1DIR)$(DFSEP).exists $(INST_MAN3DIR)$(DFSEP).exists
++ $(NOECHO) $(NOOP)
++
++# Backwards compat with 6.18 through 6.25
++blibdirs.ts : blibdirs
++ $(NOECHO) $(NOOP)
++
++$(INST_LIBDIR)$(DFSEP).exists :: Makefile.PL
++ $(NOECHO) $(MKPATH) $(INST_LIBDIR)
++ $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_LIBDIR)
++ $(NOECHO) $(TOUCH) $(INST_LIBDIR)$(DFSEP).exists
++
++$(INST_ARCHLIB)$(DFSEP).exists :: Makefile.PL
++ $(NOECHO) $(MKPATH) $(INST_ARCHLIB)
++ $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_ARCHLIB)
++ $(NOECHO) $(TOUCH) $(INST_ARCHLIB)$(DFSEP).exists
++
++$(INST_AUTODIR)$(DFSEP).exists :: Makefile.PL
++ $(NOECHO) $(MKPATH) $(INST_AUTODIR)
++ $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_AUTODIR)
++ $(NOECHO) $(TOUCH) $(INST_AUTODIR)$(DFSEP).exists
++
++$(INST_ARCHAUTODIR)$(DFSEP).exists :: Makefile.PL
++ $(NOECHO) $(MKPATH) $(INST_ARCHAUTODIR)
++ $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_ARCHAUTODIR)
++ $(NOECHO) $(TOUCH) $(INST_ARCHAUTODIR)$(DFSEP).exists
++
++$(INST_BIN)$(DFSEP).exists :: Makefile.PL
++ $(NOECHO) $(MKPATH) $(INST_BIN)
++ $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_BIN)
++ $(NOECHO) $(TOUCH) $(INST_BIN)$(DFSEP).exists
++
++$(INST_SCRIPT)$(DFSEP).exists :: Makefile.PL
++ $(NOECHO) $(MKPATH) $(INST_SCRIPT)
++ $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_SCRIPT)
++ $(NOECHO) $(TOUCH) $(INST_SCRIPT)$(DFSEP).exists
++
++$(INST_MAN1DIR)$(DFSEP).exists :: Makefile.PL
++ $(NOECHO) $(MKPATH) $(INST_MAN1DIR)
++ $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_MAN1DIR)
++ $(NOECHO) $(TOUCH) $(INST_MAN1DIR)$(DFSEP).exists
++
++$(INST_MAN3DIR)$(DFSEP).exists :: Makefile.PL
++ $(NOECHO) $(MKPATH) $(INST_MAN3DIR)
++ $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_MAN3DIR)
++ $(NOECHO) $(TOUCH) $(INST_MAN3DIR)$(DFSEP).exists
++
++
++
++# --- MakeMaker linkext section:
++
++linkext :: $(LINKTYPE)
++ $(NOECHO) $(NOOP)
++
++
++# --- MakeMaker dlsyms section:
++
++
++# --- MakeMaker dynamic section:
++
++dynamic :: $(FIRST_MAKEFILE) $(INST_DYNAMIC) $(INST_BOOT)
++ $(NOECHO) $(NOOP)
++
++
++# --- MakeMaker dynamic_bs section:
++BOOTSTRAP = $(BASEEXT).bs
++
++# As Mkbootstrap might not write a file (if none is required)
++# we use touch to prevent make continually trying to remake it.
++# The DynaLoader only reads a non-empty file.
++$(BOOTSTRAP) : $(FIRST_MAKEFILE) $(BOOTDEP) $(INST_ARCHAUTODIR)$(DFSEP).exists
++ $(NOECHO) $(ECHO) "Running Mkbootstrap for $(NAME) ($(BSLOADLIBS))"
++ $(NOECHO) $(PERLRUN) \
++ "-MExtUtils::Mkbootstrap" \
++ -e "Mkbootstrap('$(BASEEXT)','$(BSLOADLIBS)');"
++ $(NOECHO) $(TOUCH) $@
++ $(CHMOD) $(PERM_RW) $@
++
++$(INST_BOOT) : $(BOOTSTRAP) $(INST_ARCHAUTODIR)$(DFSEP).exists
++ $(NOECHO) $(RM_RF) $@
++ - $(CP) $(BOOTSTRAP) $@
++ $(CHMOD) $(PERM_RW) $@
++
++
++# --- MakeMaker dynamic_lib section:
++
++# This section creates the dynamically loadable $(INST_DYNAMIC)
++# from $(OBJECT) and possibly $(MYEXTLIB).
++ARMAYBE = :
++OTHERLDFLAGS =
++INST_DYNAMIC_DEP =
++INST_DYNAMIC_FIX =
++
++$(INST_DYNAMIC): $(OBJECT) $(MYEXTLIB) $(BOOTSTRAP) $(INST_ARCHAUTODIR)$(DFSEP).exists $(EXPORT_LIST) $(PERL_ARCHIVE) $(PERL_ARCHIVE_AFTER) $(INST_DYNAMIC_DEP)
++ $(RM_F) $@
++ $(LD) $(LDDLFLAGS) $(LDFROM) $(OTHERLDFLAGS) -o $@ $(MYEXTLIB) \
++ $(PERL_ARCHIVE) $(LDLOADLIBS) $(PERL_ARCHIVE_AFTER) $(EXPORT_LIST) \
++ $(INST_DYNAMIC_FIX)
++ $(CHMOD) $(PERM_RWX) $@
++
++
++# --- MakeMaker static section:
++
++## $(INST_PM) has been moved to the all: target.
++## It remains here for awhile to allow for old usage: "make static"
++static :: $(FIRST_MAKEFILE) $(INST_STATIC)
++ $(NOECHO) $(NOOP)
++
++
++# --- MakeMaker static_lib section:
++
++$(INST_STATIC) : $(OBJECT) $(MYEXTLIB) $(INST_ARCHAUTODIR)$(DFSEP).exists
++ $(RM_RF) $@
++ $(FULL_AR) $(AR_STATIC_ARGS) $@ $(OBJECT) && $(RANLIB) $@
++ $(CHMOD) $(PERM_RWX) $@
++ $(NOECHO) $(ECHO) "$(EXTRALIBS)" > $(INST_ARCHAUTODIR)/extralibs.ld
++
++
++# --- MakeMaker manifypods section:
++
++POD2MAN_EXE = $(PERLRUN) "-MExtUtils::Command::MM" -e pod2man "--"
++POD2MAN = $(POD2MAN_EXE)
++
++
++manifypods : pure_all \
++ Zerg.pm
++ $(NOECHO) $(POD2MAN) --section=$(MAN3EXT) --perm_rw=$(PERM_RW) \
++ Zerg.pm $(INST_MAN3DIR)/Zerg.$(MAN3EXT)
++
++
++
++
++# --- MakeMaker processPL section:
++
++
++# --- MakeMaker installbin section:
++
++
++# --- MakeMaker subdirs section:
++
++# The default clean, realclean and test targets in this Makefile
++# have automatically been given entries for each subdir.
++
++
++subdirs ::
++ $(NOECHO) cd Report && $(MAKE) $(USEMAKEFILE) $(FIRST_MAKEFILE) all $(PASTHRU)
++
++
++# --- MakeMaker clean_subdirs section:
++clean_subdirs :
++ $(ABSPERLRUN) -e 'chdir '\''Report'\''; system '\''$(MAKE) clean'\'' if -f '\''$(FIRST_MAKEFILE)'\'';' --
++
++
++# --- MakeMaker clean section:
++
++# Delete temporary files but do not touch installed files. We don't delete
++# the Makefile here so a later make realclean still has a makefile to use.
++
++clean :: clean_subdirs
++ - $(RM_F) \
++ *$(LIB_EXT) core \
++ core.[0-9] $(INST_ARCHAUTODIR)/extralibs.all \
++ core.[0-9][0-9] $(BASEEXT).bso \
++ pm_to_blib.ts core.[0-9][0-9][0-9][0-9] \
++ $(BASEEXT).x $(BOOTSTRAP) \
++ perl$(EXE_EXT) tmon.out \
++ Zerg.c *$(OBJ_EXT) \
++ pm_to_blib $(INST_ARCHAUTODIR)/extralibs.ld \
++ blibdirs.ts core.[0-9][0-9][0-9][0-9][0-9] \
++ *perl.core core.*perl.*.? \
++ $(MAKE_APERL_FILE) $(BASEEXT).def \
++ perl core.[0-9][0-9][0-9] \
++ mon.out lib$(BASEEXT).def \
++ perl.exe perlmain.c \
++ so_locations $(BASEEXT).exp
++ - $(RM_RF) \
++ blib
++ - $(MV) $(FIRST_MAKEFILE) $(MAKEFILE_OLD) $(DEV_NULL)
++
++
++# --- MakeMaker realclean_subdirs section:
++realclean_subdirs :
++ - $(ABSPERLRUN) -e 'chdir '\''Report'\''; system '\''$(MAKE) $(USEMAKEFILE) $(MAKEFILE_OLD) realclean'\'' if -f '\''$(MAKEFILE_OLD)'\'';' --
++ - $(ABSPERLRUN) -e 'chdir '\''Report'\''; system '\''$(MAKE) $(USEMAKEFILE) $(FIRST_MAKEFILE) realclean'\'' if -f '\''$(FIRST_MAKEFILE)'\'';' --
++
++
++# --- MakeMaker realclean section:
++# Delete temporary files (via clean) and also delete dist files
++realclean purge :: clean realclean_subdirs
++ - $(RM_F) \
++ $(OBJECT) $(MAKEFILE_OLD) \
++ $(FIRST_MAKEFILE)
++ - $(RM_RF) \
++ $(DISTVNAME)
++
++
++# --- MakeMaker metafile section:
++metafile : create_distdir
++ $(NOECHO) $(ECHO) Generating META.yml
++ $(NOECHO) $(ECHO) '--- #YAML:1.0' > META_new.yml
++ $(NOECHO) $(ECHO) 'name: Zerg' >> META_new.yml
++ $(NOECHO) $(ECHO) 'version: 1.0.4' >> META_new.yml
++ $(NOECHO) $(ECHO) 'abstract: a lexical scanner for BLAST reports.' >> META_new.yml
++ $(NOECHO) $(ECHO) 'author:' >> META_new.yml
++ $(NOECHO) $(ECHO) ' - Apuã Paquola <apua at iq.usp.br>' >> META_new.yml
++ $(NOECHO) $(ECHO) 'license: unknown' >> META_new.yml
++ $(NOECHO) $(ECHO) 'distribution_type: module' >> META_new.yml
++ $(NOECHO) $(ECHO) 'configure_requires:' >> META_new.yml
++ $(NOECHO) $(ECHO) ' ExtUtils::MakeMaker: 0' >> META_new.yml
++ $(NOECHO) $(ECHO) 'build_requires:' >> META_new.yml
++ $(NOECHO) $(ECHO) ' ExtUtils::MakeMaker: 0' >> META_new.yml
++ $(NOECHO) $(ECHO) 'requires: {}' >> META_new.yml
++ $(NOECHO) $(ECHO) 'no_index:' >> META_new.yml
++ $(NOECHO) $(ECHO) ' directory:' >> META_new.yml
++ $(NOECHO) $(ECHO) ' - t' >> META_new.yml
++ $(NOECHO) $(ECHO) ' - inc' >> META_new.yml
++ $(NOECHO) $(ECHO) 'generated_by: ExtUtils::MakeMaker version 6.55_02' >> META_new.yml
++ $(NOECHO) $(ECHO) 'meta-spec:' >> META_new.yml
++ $(NOECHO) $(ECHO) ' url: http://module-build.sourceforge.net/META-spec-v1.4.html' >> META_new.yml
++ $(NOECHO) $(ECHO) ' version: 1.4' >> META_new.yml
++ -$(NOECHO) $(MV) META_new.yml $(DISTVNAME)/META.yml
++
++
++# --- MakeMaker signature section:
++signature :
++ cpansign -s
++
++
++# --- MakeMaker dist_basics section:
++distclean :: realclean distcheck
++ $(NOECHO) $(NOOP)
++
++distcheck :
++ $(PERLRUN) "-MExtUtils::Manifest=fullcheck" -e fullcheck
++
++skipcheck :
++ $(PERLRUN) "-MExtUtils::Manifest=skipcheck" -e skipcheck
++
++manifest :
++ $(PERLRUN) "-MExtUtils::Manifest=mkmanifest" -e mkmanifest
++
++veryclean : realclean
++ $(RM_F) *~ */*~ *.orig */*.orig *.bak */*.bak *.old */*.old
++
++
++
++# --- MakeMaker dist_core section:
++
++dist : $(DIST_DEFAULT) $(FIRST_MAKEFILE)
++ $(NOECHO) $(ABSPERLRUN) -l -e 'print '\''Warning: Makefile possibly out of date with $(VERSION_FROM)'\''' \
++ -e ' if -e '\''$(VERSION_FROM)'\'' and -M '\''$(VERSION_FROM)'\'' < -M '\''$(FIRST_MAKEFILE)'\'';' --
++
++tardist : $(DISTVNAME).tar$(SUFFIX)
++ $(NOECHO) $(NOOP)
++
++uutardist : $(DISTVNAME).tar$(SUFFIX)
++ uuencode $(DISTVNAME).tar$(SUFFIX) $(DISTVNAME).tar$(SUFFIX) > $(DISTVNAME).tar$(SUFFIX)_uu
++
++$(DISTVNAME).tar$(SUFFIX) : distdir
++ $(PREOP)
++ $(TO_UNIX)
++ $(TAR) $(TARFLAGS) $(DISTVNAME).tar $(DISTVNAME)
++ $(RM_RF) $(DISTVNAME)
++ $(COMPRESS) $(DISTVNAME).tar
++ $(POSTOP)
++
++zipdist : $(DISTVNAME).zip
++ $(NOECHO) $(NOOP)
++
++$(DISTVNAME).zip : distdir
++ $(PREOP)
++ $(ZIP) $(ZIPFLAGS) $(DISTVNAME).zip $(DISTVNAME)
++ $(RM_RF) $(DISTVNAME)
++ $(POSTOP)
++
++shdist : distdir
++ $(PREOP)
++ $(SHAR) $(DISTVNAME) > $(DISTVNAME).shar
++ $(RM_RF) $(DISTVNAME)
++ $(POSTOP)
++
++
++# --- MakeMaker distdir section:
++create_distdir :
++ $(RM_RF) $(DISTVNAME)
++ $(PERLRUN) "-MExtUtils::Manifest=manicopy,maniread" \
++ -e "manicopy(maniread(),'$(DISTVNAME)', '$(DIST_CP)');"
++
++distdir : create_distdir distmeta
++ $(NOECHO) $(NOOP)
++
++
++
++# --- MakeMaker dist_test section:
++disttest : distdir
++ cd $(DISTVNAME) && $(ABSPERLRUN) Makefile.PL "INSTALLDIRS=vendor"
++ cd $(DISTVNAME) && $(MAKE) $(PASTHRU)
++ cd $(DISTVNAME) && $(MAKE) test $(PASTHRU)
++
++
++
++# --- MakeMaker dist_ci section:
++
++ci :
++ $(PERLRUN) "-MExtUtils::Manifest=maniread" \
++ -e "@all = keys %{ maniread() };" \
++ -e "print(qq{Executing $(CI) @all\n}); system(qq{$(CI) @all});" \
++ -e "print(qq{Executing $(RCS_LABEL) ...\n}); system(qq{$(RCS_LABEL) @all});"
++
++
++# --- MakeMaker distmeta section:
++distmeta : create_distdir metafile
++ $(NOECHO) cd $(DISTVNAME) && $(ABSPERLRUN) -MExtUtils::Manifest=maniadd -e 'eval { maniadd({q{META.yml} => q{Module meta-data (added by MakeMaker)}}) } ' \
++ -e ' or print "Could not add META.yml to MANIFEST: $${'\''@'\''}\n"' --
++
++
++
++# --- MakeMaker distsignature section:
++distsignature : create_distdir
++ $(NOECHO) cd $(DISTVNAME) && $(ABSPERLRUN) -MExtUtils::Manifest=maniadd -e 'eval { maniadd({q{SIGNATURE} => q{Public-key signature (added by MakeMaker)}}) } ' \
++ -e ' or print "Could not add SIGNATURE to MANIFEST: $${'\''@'\''}\n"' --
++ $(NOECHO) cd $(DISTVNAME) && $(TOUCH) SIGNATURE
++ cd $(DISTVNAME) && cpansign -s
++
++
++
++# --- MakeMaker install section:
++
++install :: pure_install doc_install
++ $(NOECHO) $(NOOP)
++
++install_perl :: pure_perl_install doc_perl_install
++ $(NOECHO) $(NOOP)
++
++install_site :: pure_site_install doc_site_install
++ $(NOECHO) $(NOOP)
++
++install_vendor :: pure_vendor_install doc_vendor_install
++ $(NOECHO) $(NOOP)
++
++pure_install :: pure_$(INSTALLDIRS)_install
++ $(NOECHO) $(NOOP)
++
++doc_install :: doc_$(INSTALLDIRS)_install
++ $(NOECHO) $(NOOP)
++
++pure__install : pure_site_install
++ $(NOECHO) $(ECHO) INSTALLDIRS not defined, defaulting to INSTALLDIRS=site
++
++doc__install : doc_site_install
++ $(NOECHO) $(ECHO) INSTALLDIRS not defined, defaulting to INSTALLDIRS=site
++
++pure_perl_install :: all
++ $(NOECHO) umask 022; $(MOD_INSTALL) \
++ $(INST_LIB) $(DESTINSTALLPRIVLIB) \
++ $(INST_ARCHLIB) $(DESTINSTALLARCHLIB) \
++ $(INST_BIN) $(DESTINSTALLBIN) \
++ $(INST_SCRIPT) $(DESTINSTALLSCRIPT) \
++ $(INST_MAN1DIR) $(DESTINSTALLMAN1DIR) \
++ $(INST_MAN3DIR) $(DESTINSTALLMAN3DIR)
++ $(NOECHO) $(WARN_IF_OLD_PACKLIST) \
++ $(SITEARCHEXP)/auto/$(FULLEXT)
++
++
++pure_site_install :: all
++ $(NOECHO) umask 02; $(MOD_INSTALL) \
++ read $(SITEARCHEXP)/auto/$(FULLEXT)/.packlist \
++ write $(DESTINSTALLSITEARCH)/auto/$(FULLEXT)/.packlist \
++ $(INST_LIB) $(DESTINSTALLSITELIB) \
++ $(INST_ARCHLIB) $(DESTINSTALLSITEARCH) \
++ $(INST_BIN) $(DESTINSTALLSITEBIN) \
++ $(INST_SCRIPT) $(DESTINSTALLSITESCRIPT) \
++ $(INST_MAN1DIR) $(DESTINSTALLSITEMAN1DIR) \
++ $(INST_MAN3DIR) $(DESTINSTALLSITEMAN3DIR)
++ $(NOECHO) $(WARN_IF_OLD_PACKLIST) \
++ $(PERL_ARCHLIB)/auto/$(FULLEXT)
++
++pure_vendor_install :: all
++ $(NOECHO) umask 022; $(MOD_INSTALL) \
++ $(INST_LIB) $(DESTINSTALLVENDORLIB) \
++ $(INST_ARCHLIB) $(DESTINSTALLVENDORARCH) \
++ $(INST_BIN) $(DESTINSTALLVENDORBIN) \
++ $(INST_SCRIPT) $(DESTINSTALLVENDORSCRIPT) \
++ $(INST_MAN1DIR) $(DESTINSTALLVENDORMAN1DIR) \
++ $(INST_MAN3DIR) $(DESTINSTALLVENDORMAN3DIR)
++
++doc_perl_install :: all
++
++doc_site_install :: all
++ $(NOECHO) $(ECHO) Appending installation info to $(DESTINSTALLSITEARCH)/perllocal.pod
++ -$(NOECHO) umask 02; $(MKPATH) $(DESTINSTALLSITEARCH)
++ -$(NOECHO) umask 02; $(DOC_INSTALL) \
++ "Module" "$(NAME)" \
++ "installed into" "$(INSTALLSITELIB)" \
++ LINKTYPE "$(LINKTYPE)" \
++ VERSION "$(VERSION)" \
++ EXE_FILES "$(EXE_FILES)" \
++ >> $(DESTINSTALLSITEARCH)/perllocal.pod
++
++doc_vendor_install :: all
++
++
++uninstall :: uninstall_from_$(INSTALLDIRS)dirs
++ $(NOECHO) $(NOOP)
++
++uninstall_from_perldirs ::
++
++uninstall_from_sitedirs ::
++ $(NOECHO) $(UNINSTALL) $(SITEARCHEXP)/auto/$(FULLEXT)/.packlist
++
++uninstall_from_vendordirs ::
++
++
++
++# --- MakeMaker force section:
++# Phony target to force checking subdirectories.
++FORCE :
++ $(NOECHO) $(NOOP)
++
++
++# --- MakeMaker perldepend section:
++
++PERL_HDRS = \
++ $(PERL_INC)/EXTERN.h \
++ $(PERL_INC)/INTERN.h \
++ $(PERL_INC)/XSUB.h \
++ $(PERL_INC)/av.h \
++ $(PERL_INC)/cc_runtime.h \
++ $(PERL_INC)/config.h \
++ $(PERL_INC)/cop.h \
++ $(PERL_INC)/cv.h \
++ $(PERL_INC)/dosish.h \
++ $(PERL_INC)/embed.h \
++ $(PERL_INC)/embedvar.h \
++ $(PERL_INC)/fakethr.h \
++ $(PERL_INC)/form.h \
++ $(PERL_INC)/gv.h \
++ $(PERL_INC)/handy.h \
++ $(PERL_INC)/hv.h \
++ $(PERL_INC)/intrpvar.h \
++ $(PERL_INC)/iperlsys.h \
++ $(PERL_INC)/keywords.h \
++ $(PERL_INC)/mg.h \
++ $(PERL_INC)/nostdio.h \
++ $(PERL_INC)/op.h \
++ $(PERL_INC)/opcode.h \
++ $(PERL_INC)/patchlevel.h \
++ $(PERL_INC)/perl.h \
++ $(PERL_INC)/perlio.h \
++ $(PERL_INC)/perlsdio.h \
++ $(PERL_INC)/perlsfio.h \
++ $(PERL_INC)/perlvars.h \
++ $(PERL_INC)/perly.h \
++ $(PERL_INC)/pp.h \
++ $(PERL_INC)/pp_proto.h \
++ $(PERL_INC)/proto.h \
++ $(PERL_INC)/regcomp.h \
++ $(PERL_INC)/regexp.h \
++ $(PERL_INC)/regnodes.h \
++ $(PERL_INC)/scope.h \
++ $(PERL_INC)/sv.h \
++ $(PERL_INC)/thread.h \
++ $(PERL_INC)/unixish.h \
++ $(PERL_INC)/util.h
++
++$(OBJECT) : $(PERL_HDRS)
++
++Zerg.c : $(XSUBPPDEPS)
++
++
++# --- MakeMaker makefile section:
++
++$(OBJECT) : $(FIRST_MAKEFILE)
++
++# We take a very conservative approach here, but it's worth it.
++# We move Makefile to Makefile.old here to avoid gnu make looping.
++$(FIRST_MAKEFILE) : Makefile.PL $(CONFIGDEP)
++ $(NOECHO) $(ECHO) "Makefile out-of-date with respect to $?"
++ $(NOECHO) $(ECHO) "Cleaning current config before rebuilding Makefile..."
++ -$(NOECHO) $(RM_F) $(MAKEFILE_OLD)
++ -$(NOECHO) $(MV) $(FIRST_MAKEFILE) $(MAKEFILE_OLD)
++ - $(MAKE) $(USEMAKEFILE) $(MAKEFILE_OLD) clean $(DEV_NULL)
++ $(PERLRUN) Makefile.PL "INSTALLDIRS=vendor"
++ $(NOECHO) $(ECHO) "==> Your Makefile has been rebuilt. <=="
++ $(NOECHO) $(ECHO) "==> Please rerun the $(MAKE) command. <=="
++ $(FALSE)
++
++
++
++# --- MakeMaker staticmake section:
++
++# --- MakeMaker makeaperl section ---
++MAP_TARGET = perl
++FULLPERL = /usr/bin/perl
++
++$(MAP_TARGET) :: static $(MAKE_APERL_FILE)
++ $(MAKE) $(USEMAKEFILE) $(MAKE_APERL_FILE) $@
++
++$(MAKE_APERL_FILE) : $(FIRST_MAKEFILE) pm_to_blib
++ $(NOECHO) $(ECHO) Writing \"$(MAKE_APERL_FILE)\" for this $(MAP_TARGET)
++ $(NOECHO) $(PERLRUNINST) \
++ Makefile.PL DIR=Report \
++ MAKEFILE=$(MAKE_APERL_FILE) LINKTYPE=static \
++ MAKEAPERL=1 NORECURS=1 CCCDLFLAGS= \
++ INSTALLDIRS=vendor
++
++
++# --- MakeMaker test section:
++
++TEST_VERBOSE=0
++TEST_TYPE=test_$(LINKTYPE)
++TEST_FILE = test.pl
++TEST_FILES =
++TESTDB_SW = -d
++
++testdb :: testdb_$(LINKTYPE)
++
++test :: $(TEST_TYPE) subdirs-test
++
++subdirs-test ::
++ $(NOECHO) $(NOOP)
++
++subdirs-test ::
++ $(NOECHO) cd Report && $(MAKE) test $(PASTHRU)
++
++
++test_dynamic :: pure_all
++ PERL_DL_NONLAZY=1 $(FULLPERLRUN) "-I$(INST_LIB)" "-I$(INST_ARCHLIB)" $(TEST_FILE)
++
++testdb_dynamic :: pure_all
++ PERL_DL_NONLAZY=1 $(FULLPERLRUN) $(TESTDB_SW) "-I$(INST_LIB)" "-I$(INST_ARCHLIB)" $(TEST_FILE)
++
++test_ : test_dynamic
++
++test_static :: pure_all $(MAP_TARGET)
++ PERL_DL_NONLAZY=1 ./$(MAP_TARGET) "-I$(INST_LIB)" "-I$(INST_ARCHLIB)" $(TEST_FILE)
++
++testdb_static :: pure_all $(MAP_TARGET)
++ PERL_DL_NONLAZY=1 ./$(MAP_TARGET) $(TESTDB_SW) "-I$(INST_LIB)" "-I$(INST_ARCHLIB)" $(TEST_FILE)
++
++
++
++# --- MakeMaker ppd section:
++# Creates a PPD (Perl Package Description) for a binary distribution.
++ppd :
++ $(NOECHO) $(ECHO) '<SOFTPKG NAME="$(DISTNAME)" VERSION="1.0.4">' > $(DISTNAME).ppd
++ $(NOECHO) $(ECHO) ' <ABSTRACT>a lexical scanner for BLAST reports.</ABSTRACT>' >> $(DISTNAME).ppd
++ $(NOECHO) $(ECHO) ' <AUTHOR>Apuã Paquola <apua at iq.usp.br></AUTHOR>' >> $(DISTNAME).ppd
++ $(NOECHO) $(ECHO) ' <IMPLEMENTATION>' >> $(DISTNAME).ppd
++ $(NOECHO) $(ECHO) ' <ARCHITECTURE NAME="x86_64-linux-gnu-thread-multi-5.10" />' >> $(DISTNAME).ppd
++ $(NOECHO) $(ECHO) ' <CODEBASE HREF="" />' >> $(DISTNAME).ppd
++ $(NOECHO) $(ECHO) ' </IMPLEMENTATION>' >> $(DISTNAME).ppd
++ $(NOECHO) $(ECHO) '</SOFTPKG>' >> $(DISTNAME).ppd
++
++
++# --- MakeMaker pm_to_blib section:
++
++pm_to_blib : $(FIRST_MAKEFILE) $(TO_INST_PM)
++ $(NOECHO) $(ABSPERLRUN) -MExtUtils::Install -e 'pm_to_blib({@ARGV}, '\''$(INST_LIB)/auto'\'', q[$(PM_FILTER)], '\''$(PERM_DIR)'\'')' -- \
++ Zerg.pm $(INST_LIB)/Zerg.pm
++ $(NOECHO) $(TOUCH) pm_to_blib
++
++
++# --- MakeMaker selfdocument section:
++
++
++# --- MakeMaker postamble section:
++
++
++# End.
+--- /dev/null
++++ libzerg-perl-1.0.4/Zerg/Report/Makefile.old
+@@ -0,0 +1,602 @@
++# This Makefile is for the Zerg::Report extension to perl.
++#
++# It was generated automatically by MakeMaker version
++# 6.55_02 (Revision: 65502) from the contents of
++# Makefile.PL. Don't edit this file, edit Makefile.PL instead.
++#
++# ANY CHANGES MADE HERE WILL BE LOST!
++#
++# MakeMaker ARGV: (q[INSTALLDIRS=vendor])
++#
++
++# MakeMaker Parameters:
++
++# ABSTRACT_FROM => q[Report.pm]
++# AUTHOR => q[Abimael A. Machado <abimael at iq.usp.br>]
++# BUILD_REQUIRES => { }
++# NAME => q[Zerg::Report]
++# PREREQ_PM => { }
++# VERSION_FROM => q[Report.pm]
++
++# --- MakeMaker post_initialize section:
++
++
++# --- MakeMaker const_config section:
++
++# These definitions are from config.sh (via /usr/lib/perl/5.10/Config.pm).
++# They may have been overridden via Makefile.PL or on the command line.
++AR = ar
++CC = cc
++CCCDLFLAGS = -fPIC
++CCDLFLAGS = -Wl,-E
++DLEXT = so
++DLSRC = dl_dlopen.xs
++EXE_EXT =
++FULL_AR = /usr/bin/ar
++LD = cc
++LDDLFLAGS = -shared -O2 -g -L/usr/local/lib -fstack-protector
++LDFLAGS = -fstack-protector -L/usr/local/lib
++LIBC = /lib/libc-2.11.2.so
++LIB_EXT = .a
++OBJ_EXT = .o
++OSNAME = linux
++OSVERS = 2.6.32-5-amd64
++RANLIB = :
++SITELIBEXP = /usr/local/share/perl/5.10.1
++SITEARCHEXP = /usr/local/lib/perl/5.10.1
++SO = so
++VENDORARCHEXP = /usr/lib/perl5
++VENDORLIBEXP = /usr/share/perl5
++
++
++# --- MakeMaker constants section:
++AR_STATIC_ARGS = cr
++DIRFILESEP = /
++DFSEP = $(DIRFILESEP)
++NAME = Zerg::Report
++NAME_SYM = Zerg_Report
++VERSION = 1.0.4
++VERSION_MACRO = VERSION
++VERSION_SYM = 1_0_4
++DEFINE_VERSION = -D$(VERSION_MACRO)=\"$(VERSION)\"
++XS_VERSION = 1.0.4
++XS_VERSION_MACRO = XS_VERSION
++XS_DEFINE_VERSION = -D$(XS_VERSION_MACRO)=\"$(XS_VERSION)\"
++INST_ARCHLIB = ../blib/arch
++INST_SCRIPT = ../blib/script
++INST_BIN = ../blib/bin
++INST_LIB = ../blib/lib
++INST_MAN1DIR = ../blib/man1
++INST_MAN3DIR = ../blib/man3
++MAN1EXT = 1p
++MAN3EXT = 3pm
++INSTALLDIRS = site
++DESTDIR =
++PREFIX = /usr
++PERLPREFIX = $(PREFIX)
++SITEPREFIX = $(PREFIX)/local
++VENDORPREFIX = $(PREFIX)
++INSTALLPRIVLIB = $(PERLPREFIX)/share/perl/5.10
++DESTINSTALLPRIVLIB = $(DESTDIR)$(INSTALLPRIVLIB)
++INSTALLSITELIB = $(SITEPREFIX)/share/perl/5.10.1
++DESTINSTALLSITELIB = $(DESTDIR)$(INSTALLSITELIB)
++INSTALLVENDORLIB = $(VENDORPREFIX)/share/perl5
++DESTINSTALLVENDORLIB = $(DESTDIR)$(INSTALLVENDORLIB)
++INSTALLARCHLIB = $(PERLPREFIX)/lib/perl/5.10
++DESTINSTALLARCHLIB = $(DESTDIR)$(INSTALLARCHLIB)
++INSTALLSITEARCH = $(SITEPREFIX)/lib/perl/5.10.1
++DESTINSTALLSITEARCH = $(DESTDIR)$(INSTALLSITEARCH)
++INSTALLVENDORARCH = $(VENDORPREFIX)/lib/perl5
++DESTINSTALLVENDORARCH = $(DESTDIR)$(INSTALLVENDORARCH)
++INSTALLBIN = $(PERLPREFIX)/bin
++DESTINSTALLBIN = $(DESTDIR)$(INSTALLBIN)
++INSTALLSITEBIN = $(SITEPREFIX)/bin
++DESTINSTALLSITEBIN = $(DESTDIR)$(INSTALLSITEBIN)
++INSTALLVENDORBIN = $(VENDORPREFIX)/bin
++DESTINSTALLVENDORBIN = $(DESTDIR)$(INSTALLVENDORBIN)
++INSTALLSCRIPT = $(PERLPREFIX)/bin
++DESTINSTALLSCRIPT = $(DESTDIR)$(INSTALLSCRIPT)
++INSTALLSITESCRIPT = $(SITEPREFIX)/bin
++DESTINSTALLSITESCRIPT = $(DESTDIR)$(INSTALLSITESCRIPT)
++INSTALLVENDORSCRIPT = $(VENDORPREFIX)/bin
++DESTINSTALLVENDORSCRIPT = $(DESTDIR)$(INSTALLVENDORSCRIPT)
++INSTALLMAN1DIR = $(PERLPREFIX)/share/man/man1
++DESTINSTALLMAN1DIR = $(DESTDIR)$(INSTALLMAN1DIR)
++INSTALLSITEMAN1DIR = $(SITEPREFIX)/man/man1
++DESTINSTALLSITEMAN1DIR = $(DESTDIR)$(INSTALLSITEMAN1DIR)
++INSTALLVENDORMAN1DIR = $(VENDORPREFIX)/share/man/man1
++DESTINSTALLVENDORMAN1DIR = $(DESTDIR)$(INSTALLVENDORMAN1DIR)
++INSTALLMAN3DIR = $(PERLPREFIX)/share/man/man3
++DESTINSTALLMAN3DIR = $(DESTDIR)$(INSTALLMAN3DIR)
++INSTALLSITEMAN3DIR = $(SITEPREFIX)/man/man3
++DESTINSTALLSITEMAN3DIR = $(DESTDIR)$(INSTALLSITEMAN3DIR)
++INSTALLVENDORMAN3DIR = $(VENDORPREFIX)/share/man/man3
++DESTINSTALLVENDORMAN3DIR = $(DESTDIR)$(INSTALLVENDORMAN3DIR)
++PERL_LIB = /usr/share/perl/5.10
++PERL_ARCHLIB = /usr/lib/perl/5.10
++LIBPERL_A = libperl.a
++FIRST_MAKEFILE = Makefile
++MAKEFILE_OLD = Makefile.old
++MAKE_APERL_FILE = Makefile.aperl
++PERLMAINCC = $(CC)
++PERL_INC = /usr/lib/perl/5.10/CORE
++PERL = /usr/bin/perl
++FULLPERL = /usr/bin/perl
++ABSPERL = $(PERL)
++PERLRUN = $(PERL)
++FULLPERLRUN = $(FULLPERL)
++ABSPERLRUN = $(ABSPERL)
++PERLRUNINST = $(PERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)"
++FULLPERLRUNINST = $(FULLPERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)"
++ABSPERLRUNINST = $(ABSPERLRUN) "-I$(INST_ARCHLIB)" "-I$(INST_LIB)"
++PERL_CORE = 0
++PERM_DIR = 755
++PERM_RW = 644
++PERM_RWX = 755
++
++MAKEMAKER = /usr/share/perl/5.10/ExtUtils/MakeMaker.pm
++MM_VERSION = 6.55_02
++MM_REVISION = 65502
++
++# FULLEXT = Pathname for extension directory (eg Foo/Bar/Oracle).
++# BASEEXT = Basename part of FULLEXT. May be just equal FULLEXT. (eg Oracle)
++# PARENT_NAME = NAME without BASEEXT and no trailing :: (eg Foo::Bar)
++# DLBASE = Basename part of dynamic library. May be just equal BASEEXT.
++MAKE = make
++FULLEXT = Zerg/Report
++BASEEXT = Report
++PARENT_NAME = Zerg
++DLBASE = $(BASEEXT)
++VERSION_FROM = Report.pm
++OBJECT =
++LDFROM = $(OBJECT)
++LINKTYPE = dynamic
++BOOTDEP =
++
++# Handy lists of source code files:
++XS_FILES =
++C_FILES =
++O_FILES =
++H_FILES =
++MAN1PODS =
++MAN3PODS = Report.pm
++
++# Where is the Config information that we are using/depend on
++CONFIGDEP = $(PERL_ARCHLIB)$(DFSEP)Config.pm $(PERL_INC)$(DFSEP)config.h
++
++# Where to build things
++INST_LIBDIR = $(INST_LIB)/Zerg
++INST_ARCHLIBDIR = $(INST_ARCHLIB)/Zerg
++
++INST_AUTODIR = $(INST_LIB)/auto/$(FULLEXT)
++INST_ARCHAUTODIR = $(INST_ARCHLIB)/auto/$(FULLEXT)
++
++INST_STATIC =
++INST_DYNAMIC =
++INST_BOOT =
++
++# Extra linker info
++EXPORT_LIST =
++PERL_ARCHIVE =
++PERL_ARCHIVE_AFTER =
++
++
++TO_INST_PM = Report.pm
++
++PM_TO_BLIB = Report.pm \
++ $(INST_LIB)/Zerg/Report.pm
++
++
++# --- MakeMaker platform_constants section:
++MM_Unix_VERSION = 6.55_02
++PERL_MALLOC_DEF = -DPERL_EXTMALLOC_DEF -Dmalloc=Perl_malloc -Dfree=Perl_mfree -Drealloc=Perl_realloc -Dcalloc=Perl_calloc
++
++
++# --- MakeMaker tool_autosplit section:
++# Usage: $(AUTOSPLITFILE) FileToSplit AutoDirToSplitInto
++AUTOSPLITFILE = $(ABSPERLRUN) -e 'use AutoSplit; autosplit($$ARGV[0], $$ARGV[1], 0, 1, 1)' --
++
++
++
++# --- MakeMaker tool_xsubpp section:
++
++
++# --- MakeMaker tools_other section:
++SHELL = /bin/sh
++CHMOD = chmod
++CP = cp
++MV = mv
++NOOP = $(TRUE)
++NOECHO = @
++RM_F = rm -f
++RM_RF = rm -rf
++TEST_F = test -f
++TOUCH = touch
++UMASK_NULL = umask 0
++DEV_NULL = > /dev/null 2>&1
++MKPATH = $(ABSPERLRUN) -MExtUtils::Command -e 'mkpath' --
++EQUALIZE_TIMESTAMP = $(ABSPERLRUN) -MExtUtils::Command -e 'eqtime' --
++FALSE = false
++TRUE = true
++ECHO = echo
++ECHO_N = echo -n
++UNINST = 0
++VERBINST = 0
++MOD_INSTALL = $(ABSPERLRUN) -MExtUtils::Install -e 'install([ from_to => {@ARGV}, verbose => '\''$(VERBINST)'\'', uninstall_shadows => '\''$(UNINST)'\'', dir_mode => '\''$(PERM_DIR)'\'' ]);' --
++DOC_INSTALL = $(ABSPERLRUN) -MExtUtils::Command::MM -e 'perllocal_install' --
++UNINSTALL = $(ABSPERLRUN) -MExtUtils::Command::MM -e 'uninstall' --
++WARN_IF_OLD_PACKLIST = $(ABSPERLRUN) -MExtUtils::Command::MM -e 'warn_if_old_packlist' --
++MACROSTART =
++MACROEND =
++USEMAKEFILE = -f
++FIXIN = $(ABSPERLRUN) -MExtUtils::MY -e 'MY->fixin(shift)' --
++
++
++# --- MakeMaker makemakerdflt section:
++makemakerdflt : all
++ $(NOECHO) $(NOOP)
++
++
++# --- MakeMaker dist section skipped.
++
++# --- MakeMaker macro section:
++
++
++# --- MakeMaker depend section:
++
++
++# --- MakeMaker cflags section:
++
++
++# --- MakeMaker const_loadlibs section:
++
++
++# --- MakeMaker const_cccmd section:
++
++
++# --- MakeMaker post_constants section:
++
++
++# --- MakeMaker pasthru section:
++
++PASTHRU = LIBPERL_A="$(LIBPERL_A)"\
++ LINKTYPE="$(LINKTYPE)"\
++ PREFIX="$(PREFIX)"
++
++
++# --- MakeMaker special_targets section:
++.SUFFIXES : .xs .c .C .cpp .i .s .cxx .cc $(OBJ_EXT)
++
++.PHONY: all config static dynamic test linkext manifest blibdirs clean realclean disttest distdir
++
++
++
++# --- MakeMaker c_o section:
++
++
++# --- MakeMaker xs_c section:
++
++
++# --- MakeMaker xs_o section:
++
++
++# --- MakeMaker top_targets section:
++all :: pure_all manifypods
++ $(NOECHO) $(NOOP)
++
++
++pure_all :: config pm_to_blib subdirs linkext
++ $(NOECHO) $(NOOP)
++
++subdirs :: $(MYEXTLIB)
++ $(NOECHO) $(NOOP)
++
++config :: $(FIRST_MAKEFILE) blibdirs
++ $(NOECHO) $(NOOP)
++
++help :
++ perldoc ExtUtils::MakeMaker
++
++
++# --- MakeMaker blibdirs section:
++blibdirs : $(INST_LIBDIR)$(DFSEP).exists $(INST_ARCHLIB)$(DFSEP).exists $(INST_AUTODIR)$(DFSEP).exists $(INST_ARCHAUTODIR)$(DFSEP).exists $(INST_BIN)$(DFSEP).exists $(INST_SCRIPT)$(DFSEP).exists $(INST_MAN1DIR)$(DFSEP).exists $(INST_MAN3DIR)$(DFSEP).exists
++ $(NOECHO) $(NOOP)
++
++# Backwards compat with 6.18 through 6.25
++blibdirs.ts : blibdirs
++ $(NOECHO) $(NOOP)
++
++$(INST_LIBDIR)$(DFSEP).exists :: Makefile.PL
++ $(NOECHO) $(MKPATH) $(INST_LIBDIR)
++ $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_LIBDIR)
++ $(NOECHO) $(TOUCH) $(INST_LIBDIR)$(DFSEP).exists
++
++$(INST_ARCHLIB)$(DFSEP).exists :: Makefile.PL
++ $(NOECHO) $(MKPATH) $(INST_ARCHLIB)
++ $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_ARCHLIB)
++ $(NOECHO) $(TOUCH) $(INST_ARCHLIB)$(DFSEP).exists
++
++$(INST_AUTODIR)$(DFSEP).exists :: Makefile.PL
++ $(NOECHO) $(MKPATH) $(INST_AUTODIR)
++ $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_AUTODIR)
++ $(NOECHO) $(TOUCH) $(INST_AUTODIR)$(DFSEP).exists
++
++$(INST_ARCHAUTODIR)$(DFSEP).exists :: Makefile.PL
++ $(NOECHO) $(MKPATH) $(INST_ARCHAUTODIR)
++ $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_ARCHAUTODIR)
++ $(NOECHO) $(TOUCH) $(INST_ARCHAUTODIR)$(DFSEP).exists
++
++$(INST_BIN)$(DFSEP).exists :: Makefile.PL
++ $(NOECHO) $(MKPATH) $(INST_BIN)
++ $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_BIN)
++ $(NOECHO) $(TOUCH) $(INST_BIN)$(DFSEP).exists
++
++$(INST_SCRIPT)$(DFSEP).exists :: Makefile.PL
++ $(NOECHO) $(MKPATH) $(INST_SCRIPT)
++ $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_SCRIPT)
++ $(NOECHO) $(TOUCH) $(INST_SCRIPT)$(DFSEP).exists
++
++$(INST_MAN1DIR)$(DFSEP).exists :: Makefile.PL
++ $(NOECHO) $(MKPATH) $(INST_MAN1DIR)
++ $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_MAN1DIR)
++ $(NOECHO) $(TOUCH) $(INST_MAN1DIR)$(DFSEP).exists
++
++$(INST_MAN3DIR)$(DFSEP).exists :: Makefile.PL
++ $(NOECHO) $(MKPATH) $(INST_MAN3DIR)
++ $(NOECHO) $(CHMOD) $(PERM_DIR) $(INST_MAN3DIR)
++ $(NOECHO) $(TOUCH) $(INST_MAN3DIR)$(DFSEP).exists
++
++
++
++# --- MakeMaker linkext section:
++
++linkext :: $(LINKTYPE)
++ $(NOECHO) $(NOOP)
++
++
++# --- MakeMaker dlsyms section:
++
++
++# --- MakeMaker dynamic section:
++
++dynamic :: $(FIRST_MAKEFILE) $(INST_DYNAMIC) $(INST_BOOT)
++ $(NOECHO) $(NOOP)
++
++
++# --- MakeMaker dynamic_bs section:
++
++BOOTSTRAP =
++
++
++# --- MakeMaker dynamic_lib section:
++
++
++# --- MakeMaker static section:
++
++## $(INST_PM) has been moved to the all: target.
++## It remains here for awhile to allow for old usage: "make static"
++static :: $(FIRST_MAKEFILE) $(INST_STATIC)
++ $(NOECHO) $(NOOP)
++
++
++# --- MakeMaker static_lib section:
++
++
++# --- MakeMaker manifypods section:
++
++POD2MAN_EXE = $(PERLRUN) "-MExtUtils::Command::MM" -e pod2man "--"
++POD2MAN = $(POD2MAN_EXE)
++
++
++manifypods : pure_all \
++ Report.pm
++ $(NOECHO) $(POD2MAN) --section=$(MAN3EXT) --perm_rw=$(PERM_RW) \
++ Report.pm $(INST_MAN3DIR)/Zerg::Report.$(MAN3EXT)
++
++
++
++
++# --- MakeMaker processPL section:
++
++
++# --- MakeMaker installbin section:
++
++
++# --- MakeMaker subdirs section:
++
++# none
++
++# --- MakeMaker clean_subdirs section:
++clean_subdirs :
++ $(NOECHO) $(NOOP)
++
++
++# --- MakeMaker clean section:
++
++# Delete temporary files but do not touch installed files. We don't delete
++# the Makefile here so a later make realclean still has a makefile to use.
++
++clean :: clean_subdirs
++ - $(RM_F) \
++ *$(LIB_EXT) core \
++ core.[0-9] $(INST_ARCHAUTODIR)/extralibs.all \
++ core.[0-9][0-9] $(BASEEXT).bso \
++ pm_to_blib.ts core.[0-9][0-9][0-9][0-9] \
++ $(BASEEXT).x $(BOOTSTRAP) \
++ perl$(EXE_EXT) tmon.out \
++ *$(OBJ_EXT) pm_to_blib \
++ $(INST_ARCHAUTODIR)/extralibs.ld blibdirs.ts \
++ core.[0-9][0-9][0-9][0-9][0-9] *perl.core \
++ core.*perl.*.? $(MAKE_APERL_FILE) \
++ perl $(BASEEXT).def \
++ core.[0-9][0-9][0-9] mon.out \
++ lib$(BASEEXT).def perlmain.c \
++ perl.exe so_locations \
++ $(BASEEXT).exp
++ - $(RM_RF) \
++ blib
++ - $(MV) $(FIRST_MAKEFILE) $(MAKEFILE_OLD) $(DEV_NULL)
++
++
++# --- MakeMaker realclean_subdirs section:
++realclean_subdirs :
++ $(NOECHO) $(NOOP)
++
++
++# --- MakeMaker realclean section:
++# Delete temporary files (via clean) and also delete dist files
++realclean purge :: clean realclean_subdirs
++ - $(RM_F) \
++ $(MAKEFILE_OLD) $(FIRST_MAKEFILE)
++ - $(RM_RF) \
++ $(DISTVNAME)
++
++
++# --- MakeMaker metafile section:
++metafile : create_distdir
++ $(NOECHO) $(ECHO) Generating META.yml
++ $(NOECHO) $(ECHO) '--- #YAML:1.0' > META_new.yml
++ $(NOECHO) $(ECHO) 'name: Zerg-Report' >> META_new.yml
++ $(NOECHO) $(ECHO) 'version: 1.0.4' >> META_new.yml
++ $(NOECHO) $(ECHO) 'abstract: get attributes from a BLAST file in a data structure' >> META_new.yml
++ $(NOECHO) $(ECHO) 'author:' >> META_new.yml
++ $(NOECHO) $(ECHO) ' - Abimael A. Machado <abimael at iq.usp.br>' >> META_new.yml
++ $(NOECHO) $(ECHO) 'license: unknown' >> META_new.yml
++ $(NOECHO) $(ECHO) 'distribution_type: module' >> META_new.yml
++ $(NOECHO) $(ECHO) 'configure_requires:' >> META_new.yml
++ $(NOECHO) $(ECHO) ' ExtUtils::MakeMaker: 0' >> META_new.yml
++ $(NOECHO) $(ECHO) 'build_requires:' >> META_new.yml
++ $(NOECHO) $(ECHO) ' ExtUtils::MakeMaker: 0' >> META_new.yml
++ $(NOECHO) $(ECHO) 'requires: {}' >> META_new.yml
++ $(NOECHO) $(ECHO) 'no_index:' >> META_new.yml
++ $(NOECHO) $(ECHO) ' directory:' >> META_new.yml
++ $(NOECHO) $(ECHO) ' - t' >> META_new.yml
++ $(NOECHO) $(ECHO) ' - inc' >> META_new.yml
++ $(NOECHO) $(ECHO) 'generated_by: ExtUtils::MakeMaker version 6.55_02' >> META_new.yml
++ $(NOECHO) $(ECHO) 'meta-spec:' >> META_new.yml
++ $(NOECHO) $(ECHO) ' url: http://module-build.sourceforge.net/META-spec-v1.4.html' >> META_new.yml
++ $(NOECHO) $(ECHO) ' version: 1.4' >> META_new.yml
++ -$(NOECHO) $(MV) META_new.yml $(DISTVNAME)/META.yml
++
++
++# --- MakeMaker signature section:
++signature :
++ cpansign -s
++
++
++# --- MakeMaker dist_basics section skipped.
++
++# --- MakeMaker dist_core section skipped.
++
++# --- MakeMaker distdir section skipped.
++
++# --- MakeMaker dist_test section skipped.
++
++# --- MakeMaker dist_ci section skipped.
++
++# --- MakeMaker distmeta section:
++distmeta : create_distdir metafile
++ $(NOECHO) cd $(DISTVNAME) && $(ABSPERLRUN) -MExtUtils::Manifest=maniadd -e 'eval { maniadd({q{META.yml} => q{Module meta-data (added by MakeMaker)}}) } ' \
++ -e ' or print "Could not add META.yml to MANIFEST: $${'\''@'\''}\n"' --
++
++
++
++# --- MakeMaker distsignature section:
++distsignature : create_distdir
++ $(NOECHO) cd $(DISTVNAME) && $(ABSPERLRUN) -MExtUtils::Manifest=maniadd -e 'eval { maniadd({q{SIGNATURE} => q{Public-key signature (added by MakeMaker)}}) } ' \
++ -e ' or print "Could not add SIGNATURE to MANIFEST: $${'\''@'\''}\n"' --
++ $(NOECHO) cd $(DISTVNAME) && $(TOUCH) SIGNATURE
++ cd $(DISTVNAME) && cpansign -s
++
++
++
++# --- MakeMaker install section skipped.
++
++# --- MakeMaker force section:
++# Phony target to force checking subdirectories.
++FORCE :
++ $(NOECHO) $(NOOP)
++
++
++# --- MakeMaker perldepend section:
++
++
++# --- MakeMaker makefile section:
++# We take a very conservative approach here, but it's worth it.
++# We move Makefile to Makefile.old here to avoid gnu make looping.
++$(FIRST_MAKEFILE) : Makefile.PL $(CONFIGDEP)
++ $(NOECHO) $(ECHO) "Makefile out-of-date with respect to $?"
++ $(NOECHO) $(ECHO) "Cleaning current config before rebuilding Makefile..."
++ -$(NOECHO) $(RM_F) $(MAKEFILE_OLD)
++ -$(NOECHO) $(MV) $(FIRST_MAKEFILE) $(MAKEFILE_OLD)
++ - $(MAKE) $(USEMAKEFILE) $(MAKEFILE_OLD) clean $(DEV_NULL)
++ $(PERLRUN) Makefile.PL "INSTALLDIRS=vendor"
++ $(NOECHO) $(ECHO) "==> Your Makefile has been rebuilt. <=="
++ $(NOECHO) $(ECHO) "==> Please rerun the $(MAKE) command. <=="
++ $(FALSE)
++
++
++
++# --- MakeMaker staticmake section:
++
++# --- MakeMaker makeaperl section ---
++MAP_TARGET = ../perl
++FULLPERL = /usr/bin/perl
++
++
++# --- MakeMaker test section:
++
++TEST_VERBOSE=0
++TEST_TYPE=test_$(LINKTYPE)
++TEST_FILE = test.pl
++TEST_FILES =
++TESTDB_SW = -d
++
++testdb :: testdb_$(LINKTYPE)
++
++test :: $(TEST_TYPE) subdirs-test
++
++subdirs-test ::
++ $(NOECHO) $(NOOP)
++
++
++test_dynamic :: pure_all
++ PERL_DL_NONLAZY=1 $(FULLPERLRUN) "-I$(INST_LIB)" "-I$(INST_ARCHLIB)" $(TEST_FILE)
++
++testdb_dynamic :: pure_all
++ PERL_DL_NONLAZY=1 $(FULLPERLRUN) $(TESTDB_SW) "-I$(INST_LIB)" "-I$(INST_ARCHLIB)" $(TEST_FILE)
++
++test_ : test_dynamic
++
++test_static :: test_dynamic
++testdb_static :: testdb_dynamic
++
++
++# --- MakeMaker ppd section:
++# Creates a PPD (Perl Package Description) for a binary distribution.
++ppd :
++ $(NOECHO) $(ECHO) '<SOFTPKG NAME="$(DISTNAME)" VERSION="1.0.4">' > $(DISTNAME).ppd
++ $(NOECHO) $(ECHO) ' <ABSTRACT>get attributes from a BLAST file in a data structure</ABSTRACT>' >> $(DISTNAME).ppd
++ $(NOECHO) $(ECHO) ' <AUTHOR>Abimael A. Machado <abimael at iq.usp.br></AUTHOR>' >> $(DISTNAME).ppd
++ $(NOECHO) $(ECHO) ' <IMPLEMENTATION>' >> $(DISTNAME).ppd
++ $(NOECHO) $(ECHO) ' <ARCHITECTURE NAME="x86_64-linux-gnu-thread-multi-5.10" />' >> $(DISTNAME).ppd
++ $(NOECHO) $(ECHO) ' <CODEBASE HREF="" />' >> $(DISTNAME).ppd
++ $(NOECHO) $(ECHO) ' </IMPLEMENTATION>' >> $(DISTNAME).ppd
++ $(NOECHO) $(ECHO) '</SOFTPKG>' >> $(DISTNAME).ppd
++
++
++# --- MakeMaker pm_to_blib section:
++
++pm_to_blib : $(FIRST_MAKEFILE) $(TO_INST_PM)
++ $(NOECHO) $(ABSPERLRUN) -MExtUtils::Install -e 'pm_to_blib({@ARGV}, '\''$(INST_LIB)/auto'\'', q[$(PM_FILTER)], '\''$(PERM_DIR)'\'')' -- \
++ Report.pm $(INST_LIB)/Zerg/Report.pm
++ $(NOECHO) $(TOUCH) pm_to_blib
++
++
++# --- MakeMaker selfdocument section:
++
++
++# --- MakeMaker postamble section:
++
++
++# End.
Added: trunk/packages/rostlab/libzerg-perl/trunk/debian/patches/new_tokens
===================================================================
--- trunk/packages/rostlab/libzerg-perl/trunk/debian/patches/new_tokens (rev 0)
+++ trunk/packages/rostlab/libzerg-perl/trunk/debian/patches/new_tokens 2011-09-22 19:56:13 UTC (rev 7906)
@@ -0,0 +1,753 @@
+Index: libzerg-perl-1.0.4/Zerg/Zerg.pm
+===================================================================
+--- libzerg-perl-1.0.4.orig/Zerg/Zerg.pm 2011-09-22 18:39:24.701700397 +0200
++++ libzerg-perl-1.0.4/Zerg/Zerg.pm 2011-09-22 19:27:40.645700935 +0200
+@@ -1,5 +1,5 @@
+-# Copyright (C) 2002 Apuã Paquola - Instituto de Química -
+-# Universidade de São Paulo - Brasil
++# Copyright (C) 2002 Apuã Paquola - Instituto de QuÃmica -
++# Universidade de São Paulo - Brasil
+ #
+ # 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
+@@ -37,73 +37,95 @@
+ # If you do not need this, moving things directly into @EXPORT or @EXPORT_OK
+ # will save memory.
+ our %EXPORT_TAGS = ( 'all' => [ qw(
+- ALIGNMENT_LENGTH
+- BLAST_VERSION
+- DESCRIPTION_ANNOTATION
+- DESCRIPTION_EVALUE
+- DESCRIPTION_HITNAME
+- DESCRIPTION_SCORE
+- END_OF_REPORT
+- EVALUE
+- GAPS
+- IDENTITIES
+- NOHITS
+- PERCENT_IDENTITIES
+- PERCENT_POSITIVES
+- POSITIVES
+- QUERY_ANNOTATION
+- QUERY_END
+- QUERY_FRAME
+- QUERY_LENGTH
+- QUERY_NAME
+- QUERY_ORIENTATION
+- QUERY_START
+- SCORE
+- SCORE_BITS
+- SUBJECT_ANNOTATION
+- SUBJECT_END
+- SUBJECT_FRAME
+- SUBJECT_LENGTH
+- SUBJECT_NAME
+- SUBJECT_ORIENTATION
+- SUBJECT_START
+- UNMATCHED
++ ALIGNMENT_LENGTH
++ BLAST_VERSION
++ CONVERGED
++ DATABASE
++ DESCRIPTION_ANNOTATION
++ DESCRIPTION_EVALUE
++ DESCRIPTION_HITNAME
++ DESCRIPTION_SCORE
++ END_OF_REPORT
++ EVALUE
++ GAPS
++ HSP_METHOD
++ IDENTITIES
++ NOHITS
++ PERCENT_IDENTITIES
++ PERCENT_POSITIVES
++ POSITIVES
++ QUERY_ALI
++ QUERY_ANNOTATION
++ QUERY_END
++ QUERY_FRAME
++ QUERY_LENGTH
++ QUERY_NAME
++ QUERY_ORIENTATION
++ QUERY_START
++ REFERENCE
++ ROUND_NUMBER
++ ROUND_SEQ_FOUND
++ ROUND_SEQ_NEW
++ SCORE
++ SCORE_BITS
++ SEARCHING
++ SUBJECT_ALI
++ SUBJECT_ANNOTATION
++ SUBJECT_END
++ SUBJECT_FRAME
++ SUBJECT_LENGTH
++ SUBJECT_NAME
++ SUBJECT_ORIENTATION
++ SUBJECT_START
++ TAIL_OF_REPORT
++ UNMATCHED
+ ) ] );
+
+ our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );
+
+ our @EXPORT = qw(
+- ALIGNMENT_LENGTH
+- BLAST_VERSION
+- DESCRIPTION_ANNOTATION
+- DESCRIPTION_EVALUE
+- DESCRIPTION_HITNAME
+- DESCRIPTION_SCORE
+- END_OF_REPORT
+- EVALUE
+- GAPS
+- IDENTITIES
+- NOHITS
+- PERCENT_IDENTITIES
+- PERCENT_POSITIVES
+- POSITIVES
+- QUERY_ANNOTATION
+- QUERY_END
+- QUERY_FRAME
+- QUERY_LENGTH
+- QUERY_NAME
+- QUERY_ORIENTATION
+- QUERY_START
+- SCORE
+- SCORE_BITS
+- SUBJECT_ANNOTATION
+- SUBJECT_END
+- SUBJECT_FRAME
+- SUBJECT_LENGTH
+- SUBJECT_NAME
+- SUBJECT_ORIENTATION
+- SUBJECT_START
+- UNMATCHED
++ ALIGNMENT_LENGTH
++ BLAST_VERSION
++ CONVERGED
++ DATABASE
++ DESCRIPTION_ANNOTATION
++ DESCRIPTION_EVALUE
++ DESCRIPTION_HITNAME
++ DESCRIPTION_SCORE
++ END_OF_REPORT
++ EVALUE
++ GAPS
++ HSP_METHOD
++ IDENTITIES
++ NOHITS
++ PERCENT_IDENTITIES
++ PERCENT_POSITIVES
++ POSITIVES
++ QUERY_ALI
++ QUERY_ANNOTATION
++ QUERY_END
++ QUERY_FRAME
++ QUERY_LENGTH
++ QUERY_NAME
++ QUERY_ORIENTATION
++ QUERY_START
++ REFERENCE
++ ROUND_NUMBER
++ ROUND_SEQ_FOUND
++ ROUND_SEQ_NEW
++ SCORE
++ SCORE_BITS
++ SEARCHING
++ SUBJECT_ALI
++ SUBJECT_ANNOTATION
++ SUBJECT_END
++ SUBJECT_FRAME
++ SUBJECT_LENGTH
++ SUBJECT_NAME
++ SUBJECT_ORIENTATION
++ SUBJECT_START
++ TAIL_OF_REPORT
++ UNMATCHED
+ );
+ our $VERSION = '1.0.4';
+
+@@ -209,37 +231,48 @@
+
+ =head2 EXPORTED CONSTANTS (TOKEN CODES)
+
+- ALIGNMENT_LENGTH
+- BLAST_VERSION
+- DESCRIPTION_ANNOTATION
+- DESCRIPTION_EVALUE
+- DESCRIPTION_HITNAME
+- DESCRIPTION_SCORE
+- END_OF_REPORT
+- EVALUE
+- GAPS
+- IDENTITIES
+- NOHITS
+- PERCENT_IDENTITIES
+- PERCENT_POSITIVES
+- POSITIVES
+- QUERY_ANNOTATION
+- QUERY_END
+- QUERY_FRAME
+- QUERY_LENGTH
+- QUERY_NAME
+- QUERY_ORIENTATION
+- QUERY_START
+- SCORE
+- SCORE_BITS
+- SUBJECT_ANNOTATION
+- SUBJECT_END
+- SUBJECT_FRAME
+- SUBJECT_LENGTH
+- SUBJECT_NAME
+- SUBJECT_ORIENTATION
+- SUBJECT_START
+- UNMATCHED
++ ALIGNMENT_LENGTH
++ BLAST_VERSION
++ CONVERGED
++ DATABASE
++ DESCRIPTION_ANNOTATION
++ DESCRIPTION_EVALUE
++ DESCRIPTION_HITNAME
++ DESCRIPTION_SCORE
++ END_OF_REPORT
++ EVALUE
++ GAPS
++ HSP_METHOD
++ IDENTITIES
++ NOHITS
++ PERCENT_IDENTITIES
++ PERCENT_POSITIVES
++ POSITIVES
++ QUERY_ALI
++ QUERY_ANNOTATION
++ QUERY_END
++ QUERY_FRAME
++ QUERY_LENGTH
++ QUERY_NAME
++ QUERY_ORIENTATION
++ QUERY_START
++ REFERENCE
++ ROUND_NUMBER
++ ROUND_SEQ_FOUND
++ ROUND_SEQ_NEW
++ SCORE
++ SCORE_BITS
++ SEARCHING
++ SUBJECT_ALI
++ SUBJECT_ANNOTATION
++ SUBJECT_END
++ SUBJECT_FRAME
++ SUBJECT_LENGTH
++ SUBJECT_NAME
++ SUBJECT_ORIENTATION
++ SUBJECT_START
++ TAIL_OF_REPORT
++ UNMATCHED
+
+ =head2 NOTES ON THE SCANNER
+
+@@ -312,13 +345,15 @@
+ and those that are modified by the parser, namely: QUERY_LENGTH,
+ SUBJECT_LENGTH, EVALUE, GAPS.
+
+-=head1 TO DO
++=head1 TODO
+
+ Add more tokens to the scanner as the need for that appears.
+
+ =head1 AUTHOR
+
+-Apuã Paquola, IQ-USP Bioinformatics Lab, apua at iq.usp.br
++Apuã Paquola, IQ-USP Bioinformatics Lab, apua at iq.usp.br
++
++Laszlo Kajan <lkajan at rostlab.org>, Technical University of Munich, Germany
+
+ =head1 SEE ALSO
+
+Index: libzerg-perl-1.0.4/Zerg/Zerg.xs
+===================================================================
+--- libzerg-perl-1.0.4.orig/Zerg/Zerg.xs 2011-09-22 18:39:28.037700573 +0200
++++ libzerg-perl-1.0.4/Zerg/Zerg.xs 2011-09-22 19:29:10.981700675 +0200
+@@ -1,6 +1,6 @@
+ /*
+- Copyright (C) 2002 Apuã Paquola - Instituto de Química -
+- Universidade de São Paulo - Brasil
++ Copyright (C) 2002 Apuã Paquola - Instituto de QuÃmica -
++ Universidade de São Paulo - Brasil
+
+ 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
+@@ -94,7 +94,14 @@
+ }
+ switch (name[1 + 5]) {
+ case 'A':
+- if (strEQ(name + 1, "UERY_ANNOTATION")) { /* Q removed */
++ if (strEQ(name + 1, "UERY_ALI")) { /* Q removed */
++#ifdef QUERY_ALI
++ return QUERY_ALI;
++#else
++ goto not_there;
++#endif
++ }
++ else if (strEQ(name + 1, "UERY_ANNOTATION")) { /* Q removed */
+ #ifdef QUERY_ANNOTATION
+ return QUERY_ANNOTATION;
+ #else
+@@ -159,6 +166,45 @@
+ }
+
+ static double
++constant_R(char *name, int len, int arg)
++{
++ if (strEQ(name + 1, "EFERENCE")) { /* R removed */
++#ifdef REFERENCE
++ return REFERENCE;
++#else
++ goto not_there;
++#endif
++ }
++ else if (strEQ(name + 1, "OUND_NUMBER")) { /* R removed */
++#ifdef ROUND_NUMBER
++ return ROUND_NUMBER;
++#else
++ goto not_there;
++#endif
++ }
++ else if (strEQ(name + 1, "OUND_SEQ_FOUND")) { /* R removed */
++#ifdef ROUND_SEQ_FOUND
++ return ROUND_SEQ_FOUND;
++#else
++ goto not_there;
++#endif
++ }
++ else if (strEQ(name + 1, "OUND_SEQ_NEW")) { /* R removed */
++#ifdef ROUND_SEQ_NEW
++ return ROUND_SEQ_NEW;
++#else
++ goto not_there;
++#endif
++ }
++ errno = EINVAL;
++ return 0;
++
++not_there:
++ errno = ENOENT;
++ return 0;
++}
++
++static double
+ constant_SC(char *name, int len, int arg)
+ {
+ if (2 + 3 > len ) {
+@@ -200,7 +246,14 @@
+ }
+ switch (name[2 + 6]) {
+ case 'A':
+- if (strEQ(name + 2, "BJECT_ANNOTATION")) { /* SU removed */
++ if (strEQ(name + 2, "BJECT_ALI")) { /* SU removed */
++#ifdef SUBJECT_ALI
++ return SUBJECT_ALI;
++#else
++ goto not_there;
++#endif
++ }
++ else if (strEQ(name + 2, "BJECT_ANNOTATION")) { /* SU removed */
+ #ifdef SUBJECT_ANNOTATION
+ return SUBJECT_ANNOTATION;
+ #else
+@@ -270,6 +323,14 @@
+ switch (name[1 + 0]) {
+ case 'C':
+ return constant_SC(name, len, arg);
++ case 'E':
++ if (strEQ(name + 2, "ARCHING")) { /* SE removed */
++#ifdef SEARCHING
++ return SEARCHING;
++#else
++ goto not_there;
++#endif
++ }
+ case 'U':
+ return constant_SU(name, len, arg);
+ }
+@@ -284,6 +345,13 @@
+ static double
+ constant_D(char *name, int len, int arg)
+ {
++ if (strEQ(name + 1, "ATABASE")) { /* D removed */
++#ifdef DATABASE
++ return DATABASE;
++#else
++ goto not_there;
++#endif
++ }
+ if (1 + 11 >= len ) {
+ errno = EINVAL;
+ return 0;
+@@ -380,6 +448,14 @@
+ goto not_there;
+ #endif
+ }
++ case 'C':
++ if (strEQ(name + 1, "ONVERGED")) { /* C removed */
++#ifdef CONVERGED
++ return CONVERGED;
++#else
++ goto not_there;
++#endif
++ }
+ case 'D':
+ return constant_D(name, len, arg);
+ case 'E':
+@@ -392,6 +468,14 @@
+ goto not_there;
+ #endif
+ }
++ case 'H':
++ if (strEQ(name + 1, "SP_METHOD")) { /* H removed */
++#ifdef HSP_METHOD
++ return HSP_METHOD;
++#else
++ goto not_there;
++#endif
++ }
+ case 'I':
+ if (strEQ(name + 0, "IDENTITIES")) { /* removed */
+ #ifdef IDENTITIES
+@@ -412,8 +496,18 @@
+ return constant_P(name, len, arg);
+ case 'Q':
+ return constant_Q(name, len, arg);
++ case 'R':
++ return constant_R(name, len, arg);
+ case 'S':
+ return constant_S(name, len, arg);
++ case 'T':
++ if (strEQ(name + 0, "TAIL_OF_REPORT")) { /* removed */
++#ifdef TAIL_OF_REPORT
++ return TAIL_OF_REPORT;
++#else
++ goto not_there;
++#endif
++ }
+ case 'U':
+ if (strEQ(name + 0, "UNMATCHED")) { /* removed */
+ #ifdef UNMATCHED
+Index: libzerg-perl-1.0.4/Zerg/Report/Report.pm
+===================================================================
+--- libzerg-perl-1.0.4.orig/Zerg/Report/Report.pm 2011-09-22 20:24:20.213700819 +0200
++++ libzerg-perl-1.0.4/Zerg/Report/Report.pm 2011-09-22 21:07:59.350075600 +0200
+@@ -17,6 +17,7 @@
+ #
+ package Zerg::Report;
+ use strict;
++use Carp;
+ use Zerg;
+
+ our $VERSION = '1.0.4';
+@@ -30,14 +31,10 @@
+
+ my $file = shift;
+
+- my $blast_report = ();
+-
+ Zerg::zerg_open_file($file);
+
+ Zerg::zerg_unignore_all();
+
+- $self->{report} = $blast_report;
+-
+ bless $self,$class;
+
+ return $self;
+@@ -49,7 +46,7 @@
+
+ my $self=shift;
+
+- my $blast_report = $self->{report};
++ my $blast_report = undef;
+
+ my ($c,$v,$hit_counter,$hsp_counter);
+
+@@ -59,6 +56,8 @@
+
+ while((($c, $v)= Zerg::zerg_get_token()) && $c)
+ {
++ if( !defined($blast_report) ){ $blast_report = {}; }
++
+ if($c==BLAST_VERSION)
+ {
+ $blast_report->{blast_version}=$v;
+@@ -86,96 +85,104 @@
+ $blast_report->{hits}[$hit_counter]{"subject_name"}=$v;
+ }
+ elsif($c==SUBJECT_ANNOTATION)
+- {
+- $blast_report->{hits}[$hit_counter]{"subject_annotation"}=$v;
+- }
+- elsif($c==SUBJECT_LENGTH)
+- {
+- $blast_report->{hits}[$hit_counter]{"subject_length"}=$v;
+- }
+- elsif($c==SCORE_BITS)
+- {
++ {
++ $blast_report->{hits}[$hit_counter]{"subject_annotation"}=$v;
++ }
++ elsif($c==SUBJECT_LENGTH)
++ {
++ $blast_report->{hits}[$hit_counter]{"subject_length"}=$v;
++ }
++ elsif($c==SCORE_BITS)
++ {
+ $hsp_counter++;
+ $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"score_bits"}=$v;
+- }
+- elsif($c==SCORE)
+- {
+- $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"score"}=$v;
+- }
+- elsif($c==EVALUE)
+- {
+- $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"evalue"}=$v;
+- }
+- elsif($c==IDENTITIES)
+- {
+- $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"identities"}=$v;
+- }
+- elsif($c==ALIGNMENT_LENGTH)
+- {
+- $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"alignment_length"}=$v;
+- }
+- elsif($c==PERCENT_IDENTITIES)
+- {
+- $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"percent_identities"}=$v;
+- }
+- elsif($c==GAPS)
+- {
+-
+- $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"gaps"}=$v;
+- }
+- elsif($c==QUERY_ORIENTATION)
+- {
+- $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_orientation"}=$v;
+- }
+- elsif($c==SUBJECT_ORIENTATION)
+- {
+- $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"subject_orientation"}=$v;
+- }
++ }
++ elsif($c==SCORE)
++ {
++ $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"score"}=$v;
++ }
++ elsif($c==EVALUE)
++ {
++ $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"evalue"}=$v;
++ }
++ elsif($c==IDENTITIES)
++ {
++ $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"identities"}=$v;
++ }
++ elsif($c==ALIGNMENT_LENGTH)
++ {
++ $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"alignment_length"}=$v;
++ }
++ elsif($c==PERCENT_IDENTITIES)
++ {
++ $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"percent_identities"}=$v;
++ }
++ elsif($c==GAPS)
++ {
++ $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"gaps"}=$v;
++ }
++ elsif($c==QUERY_ORIENTATION)
++ {
++ $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_orientation"}=$v;
++ }
++ elsif($c==SUBJECT_ORIENTATION)
++ {
++ $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"subject_orientation"}=$v;
++ }
+ elsif($c==QUERY_START)
+ {
+- $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_start"}=$v;
+-
++ if( $v && !$blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_start"} ){ $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_start"}=$v; }
++ }
++ elsif($c==QUERY_ALI)
++ {
++ if( $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_start"} ){ $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_ali"} .= $v; }
+ }
+ elsif($c==QUERY_END)
+ {
+- $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_end"}=$v;
++ $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_end"}=$v;
+ }
+ elsif($c==SUBJECT_START)
+ {
+- $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"subject_start"}=$v;
++ if( $v && !$blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"subject_start"} ){ $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"subject_start"}=$v; }
++ }
++ elsif($c==SUBJECT_ALI)
++ {
++ if( $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_start"} ){ $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"subject_ali"} .= $v; }
+ }
+ elsif($c==SUBJECT_END)
+- {
+- $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"subject_end"}=$v;
+- }
+- elsif($c==POSITIVES)
+- {
+- $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"positives"}=$v;
+- }
+- elsif($c==PERCENT_POSITIVES)
+- {
++ {
++ $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"subject_end"}=$v;
++ }
++ elsif($c==POSITIVES)
++ {
++ $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"positives"}=$v;
++ }
++ elsif($c==PERCENT_POSITIVES)
++ {
+ $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"percent_positives"}=$v;
+- }
+- elsif($c==QUERY_FRAME)
+- {
+- $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_frame"}=$v;
+- }
+- elsif($c==SUBJECT_FRAME)
+- {
+- $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"subject_frame"}=$v;
+- }
+- elsif($c==UNMATCHED)
+- {
+- die "Syntax error in blast report\n";
+- }
+- elsif($c==END_OF_REPORT)
+- {
+- my $r=$blast_report;
+- $blast_report=();
+- return $r;
+- }
++ }
++ elsif($c==QUERY_FRAME)
++ {
++ $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"query_frame"}=$v;
++ }
++ elsif($c==SUBJECT_FRAME)
++ {
++ $blast_report->{hits}[$hit_counter]{"hsps"}[$hsp_counter]{"subject_frame"}=$v;
++ }
++ elsif($c==ROUND_NUMBER)
++ {
++ $blast_report->{round_begins}[$v-1] = $hit_counter + 1;
++ }
++ elsif($c==UNMATCHED)
++ {
++ confess("Syntax error in blast report: '$v'");
++ }
++ elsif($c==END_OF_REPORT)
++ {
++ return $blast_report;
++ }
+ }
+- return ();
++ return $blast_report;
+ }
+
+ sub closeFile
+@@ -218,8 +225,9 @@
+ foreach my $hit (@{$r->{hits}})
+ {
+ foreach my $hsp (@{$hit->{hsps}})
+- {
+- print "$r->{query_name} $hit->{subject_name} $hsp->{score_bits}\n"; }
++ {
++ print "$r->{query_name} $hit->{subject_name} $hsp->{score_bits}\n";
++ }
+ }
+ }
+
+@@ -227,15 +235,15 @@
+
+ =head1 DESCRIPTION
+
+- Zerg::Report uses Zerg to parse a file containing multiple BLAST
++ Zerg::Report uses Zerg to parse a file - or STDIN if file is not given - containing multiple BLAST
+ reports and, for each report, stores the obtained fields in a data
+ structure made of arrays and hashes. Please consult the Zerg man
+ page to see which fields are extracted.
+
+ The method getReport() reads a BLAST report from the input file and
+ returns a reference to a data structure like the one in the example
+- below. When no report is found, it returns false. It dies from
+- syntax errors in BLAST reports.
++ below. When no report is found, it returns undef. It dies from
++ syntax errors in BLAST reports with a stack backtrace.
+
+ Example of a data structure returned by getReport():
+
+@@ -245,26 +253,27 @@
+ 'byte_offset' => 4981,
+ 'query_length' => '444',
+ 'query_annotation' => ''
+-
++ 'round_begins' => [ 0, 129, 201 ], # indicates the first hit in each round of iterated blast
+ 'hits' => [
+ {
+ 'subject_annotation' => '(NC_003210) similar to cation (calcium) transporting ATPase [Listeria monocytogenes EGD-e]',
+ 'hsps' => [
+ {
+- 'query_end' => '428',
+- 'subject_end' => '151',
+- 'identities' => '59',
+- 'score' => '252',
+- 'percent_positives' => '57',
+- 'gaps' => '0',
+- 'score_bits' => '101',
+- 'alignment_length' => '142',
+- 'evalue' => '2e-21',
+- 'percent_identities' => '41',
+- 'positives' => '83',
+- 'query_start' => '3',
+- 'subject_start' => '22',
+- 'query_frame' => '+3'
++ 'query_end' => '82',
++ 'subject_ali' => 'ASELEIFAALIECEA-GSTDYDGMLAVASVVMNRVNHRYYPDTITGVIYQSGQFSPVASGKLDKVLKRGIKSSCLEVAKDA',
++ 'query_ali' => 'DAQTRKLAAIAYGEASGANDANEIGGIAWAVANRARAWGGK-TVDGLLAADPNYTYAVKDG-NQRYAKLMKATEAAIAADP',
++ 'subject_end' => '328',
++ 'identities' => '15',
++ 'score' => '87',
++ 'percent_positives' => '41',
++ 'gaps' => '3',
++ 'score_bits' => '37.9',
++ 'alignment_length' => '81',
++ 'evalue' => '0.40',
++ 'percent_identities' => '18',
++ 'positives' => '34',
++ 'query_start' => '4',
++ 'subject_start' => '249'
+ }
+ ],
+ 'subject_length' => '880',
+@@ -275,11 +284,13 @@
+
+ =head1 AUTHORS
+
+-Apuã Paquola <apua at iq.usp.br>, Abimael Machado <abimael at iq.usp.br>
+-IQ-USP Bioinformatics Lab
++Apuã Paquola <apua at iq.usp.br>, Abimael Machado <abimael at iq.usp.br> IQ-USP Bioinformatics Lab
++
++Laszlo Kajan <lkajan at rostlab.org>, Technical University of Munich
+
+ =head1 SEE ALSO
+
+ Zerg
+
+ =cut
++# vim:et:ts=2:ai:
Added: trunk/packages/rostlab/libzerg-perl/trunk/debian/patches/series
===================================================================
--- trunk/packages/rostlab/libzerg-perl/trunk/debian/patches/series (rev 0)
+++ trunk/packages/rostlab/libzerg-perl/trunk/debian/patches/series 2011-09-22 19:56:13 UTC (rev 7906)
@@ -0,0 +1,2 @@
+new_tokens
+debian-changes-1.0.4-1
More information about the debian-med-commit
mailing list