debian/genomethreader.install

-bin/* usr/bin
+bin/align_dna usr/bin
+bin/gth usr/bin
+bin/gthbssmfileinfo usr/bin
+bin/gthbssmrmsd usr/bin
+bin/gthconsensus usr/bin
+bin/gthgetseq usr/bin
+bin/gthsplit usr/bin
+bin/gthbssmbuild usr/bin
+bin/gthbssmprint usr/bin
+bin/gthbssmtrain usr/bin
+bin/gthfilestat usr/bin
+bin/gthmkbssmfiles usr/bin
 debian/bssm usr/lib/genomethreader
 debian/gthdata usr/share/genomethreader

debian/man_src/gthbssmfileinfo.1.adoc

+# gthbssmfileinfo(1)
+
+## NAME
+
+gthbssmfileinfo - show info about splice site model
+
+## SYNOPSIS
+
+*gthbssmfileinfo* [option ...] bssm_file
+
+## DESCRIPTION
+
+Show information about the specified BSSM file.
+
+## OPTIONS
+
+*-help*::
+ display help and exit
+
+*-version*::
+ display version information and exit

debian/man_src/gthbssmprint.1.adoc

+# gthbssmprint(1)
+
+## NAME
+
+gthbssmprint - print splice site model
+
+## SYNOPSIS
+
+*gthbssmprint* [option ...] bssm_file
+
+## DESCRIPTION
+
+Print BSSM file bssm_file to stdout.
+
+## OPTIONS
+
+*-help*::
+ display help and exit
+
+*-version*::
+ display version information and exit

debian/man_src/gthbssmrmsd.1.adoc

+# gthbssmrmsd(1)
+
+## NAME
+
+gthbssmrmsd - calculate distance between splice site models
+
+## SYNOPSIS
+
+*gthbssmrmsd* [option ...] BSSM_file_1 BSSM_file_2
+
+## DESCRIPTION
+
+Show RMSDs between given BSSM files.
+
+## OPTIONS
+
+*-help*::
+ display help and exit
+
+*-version*::
+ display version information and exit

debian/man_src/gthbssmtrain.1.adoc

+# gthbssmtrain(1)
+
+## NAME
+
+gthbssmtrain - train splice site model
+
+## SYNOPSIS
+
+*gthbssmtrain* [option ...] GFF3_file
+
+## DESCRIPTION
+
+Create BSSM training data from annotation given in GFF3_file.
+
+## OPTIONS
+
+*-outdir*::
+  set name of output directory to which the training files are
+                written
+                default: training_data
+
+*-gcdonor*::
+  extract training data for GC donor sites
+                default: yes
+
+*-filtertype*::
+  set type of features to used for filtering (usually 'exon' or
+                'CDS')
+                default: exon
+
+*-goodexoncount*::
+  set the minimum number of good exons a feature must have to be
+                included into the training data
+                default: 1
+
+*-cutoff*::
+  set the minimum score an exon must have to count towards the
+                ``good exon count'' (exons without a score count as good)
+                default: 1.00
+
+*-extracttype*::
+  set type of features to be extracted as exons (usually 'exon' or
+                'CDS')
+                default: CDS
+
+*-seqfile*::
+  set the sequence file from which to take the sequences
+                default: undefined
+
+*-encseq*::
+  set the encoded sequence indexname from which to take the
+                sequences
+                default: undefined
+
+*-seqfiles*::
+  set the sequence files from which to extract the features
+                use '--' to terminate the list of sequence files 
+
+*-matchdesc*::
+  search the sequence descriptions from the input files for the
+                desired sequence IDs (in GFF3), reporting the first match
+                default: no
+
+*-matchdescstart*::
+  exactly match the sequence descriptions from the input files for
+                the desired sequence IDs (in GFF3) from the beginning to the
+                first whitespace
+                default: no
+
+*-usedesc*::
+  use sequence descriptions to map the sequence IDs (in GFF3) to
+                actual sequence entries.
+                If a description contains a sequence range (e.g.,
+                III:1000001..2000000), the first  part is used as sequence ID
+                ('III') and the first range position as offset ('1000001')
+                default: no
+
+*-regionmapping*::
+  set file containing sequence-region to sequence file mapping
+                default: undefined
+
+*-seed*::
+  set seed for random number generator manually
+                0 generates a seed from the current time and the process id
+                default: 0
+
+*-v*::
+  be verbose
+                default: no
+
+*-gzip*::
+  write gzip compressed output files
+                default: no
+
+*-bzip2*::
+  write bzip2 compressed output files
+                default: no
+
+*-force*::
+  force writing to output files
+                default: no
+
+*-help*::
+  display help and exit
+
+*-version*::
+  display version information and exit

debian/man_src/gthconsensus.1.adoc

+# gthconsensus(1)
+
+## NAME
+
+gthconsensus - build consensus spliced alignments
+
+## SYNOPSIS
+
+*gthconsensus* [option ...] [file ...]
+
+## DESCRIPTION
+
+Show GenomeThreader output files containing intermediate results and assemble
+the contained spliced alignments to consensus spliced alignments.
+
+## OPTIONS
+
+*-translationtable*::
+  set the codon translation table used for codon translation in
+                   matching, DP, and output
+                   default: 1
+
+*-v*::
+  be verbose
+                   default: no
+
+*-xmlout*::
+  show output in XML format
+                   default: no
+
+*-gff3out*::
+  show output in GFF3 format
+                   default: no
+
+*-md5ids*::
+  show MD5 fingerprints as sequence IDs
+                   default: no
+
+*-o*::
+  redirect output to specified file
+                   default: undefined
+
+*-gzip*::
+  write gzip compressed output file
+                   default: no
+
+*-bzip2*::
+  write bzip2 compressed output file
+                   default: no
+
+*-force*::
+  force writing to output file
+                   default: no
+
+*-gs2out*::
+  output in old GeneSeqer2 format
+                   default: no
+
+*-minalignmentscore*::
+  set the minimum alignment score for spliced alignments to be
+                   included into the set of spliced alignments
+                   default: 0.00
+
+*-maxalignmentscore*::
+  set the maximum alignment score for spliced alignments to be
+                   included into the set of spliced alignments
+                   default: 1.00
+
+*-mincoverage*::
+  set the minimum coverage for spliced alignments to be
+                   included into the set of spliced alignments
+                   default: 0.00
+
+*-maxcoverage*::
+  set the maximum coverage for spliced alignments to be
+                   included into the set of spliced alignments
+                   default: 9999.99
+
+*-intermediate*::
+  stop after calculation of spliced alignments and output
+                   results in reusable XML format. Do not process this output
+                   yourself, use the ``normal'' XML output instead!
+                   default: no
+
+*-help*::
+  display help for basic options and exit
+
+*-help+*::
+  display help for all options and exit
+
+*-version*::
+  display version information and exit

debian/man_src/gthfilestat.1.adoc

+# gthfilestat(1)
+
+## NAME
+
+gthfilestat - show statistics about consensus spliced alignments
+
+## SYNOPSIS
+
+*gthfilestat* [option ...] [file ...]
+
+## DESCRIPTION
+
+Show statistics about spliced alignments in GenomeThreader output files
+containing intermediate results.
+
+## OPTIONS
+
+*-minalignmentscore*::
+  set the minimum alignment score for spliced alignments to be
+                   included into the set of spliced alignments
+                   default: 0.00
+
+*-maxalignmentscore*::
+  set the maximum alignment score for spliced alignments to be
+                   included into the set of spliced alignments
+                   default: 1.00
+
+*-mincoverage*::
+  set the minimum coverage for spliced alignments to be
+                   included into the set of spliced alignments
+                   default: 0.00
+
+*-maxcoverage*::
+  set the maximum coverage for spliced alignments to be
+                   included into the set of spliced alignments
+                   default: 9999.99
+
+*-v*::
+  be verbose
+                   default: no
+
+*-help*::
+  display help and exit
+
+*-version*::
+  display version information and exit

debian/man_src/gthgetseq.1.adoc

+# gthgetseq(1)
+
+## NAME
+
+gthgetseq - get FASTA sequences from GenomeThreader files
+
+## SYNOPSIS
+
+*gthgetseq* -getcdna | -getprotein | -getgenomic [option ...] [file ...]
+
+## DESCRIPTION
+
+Get FASTA sequences from GenomeThreader files containing intermediate results.
+The sequences are shown on stdout.
+
+## OPTIONS
+
+*-getcdna*::
+  get cDNA/EST sequences
+                   default: no
+
+*-getcdnacomp*::
+  get complement of cDNA/EST sequences
+                   default: no
+
+*-getprotein*::
+  get protein sequences
+                   default: no
+
+*-getproteincomp*::
+  get complement of protein sequences
+                   default: no
+
+*-getgenomic*::
+  get genomic sequences
+                   default: no
+
+*-getgenomiccomp*::
+  get complement of genomic sequences
+                   default: no
+
+*-minalignmentscore*::
+  set the minimum alignment score for spliced alignments to be
+                   included into the set of spliced alignments
+                   default: 0.00
+
+*-maxalignmentscore*::
+  set the maximum alignment score for spliced alignments to be
+                   included into the set of spliced alignments
+                   default: 1.00
+
+*-mincoverage*::
+  set the minimum coverage for spliced alignments to be
+                   included into the set of spliced alignments
+                   default: 0.00
+
+*-maxcoverage*::
+  set the maximum coverage for spliced alignments to be
+                   included into the set of spliced alignments
+                   default: 9999.99
+
+*-gzip*::
+  gzip compressed input file(s)
+                   default: no
+
+*-bzip2*::
+  bzip2 compressed input file(s)
+                   default: no
+
+*-help*::
+  display help and exit
+
+*-version*::
+  display version information and exit

debian/man_src/gthmkbssmfiles.1.adoc

+# gthmkbssmfiles(1)
+
+## NAME
+
+gthmkbssmfiles - rite hard coded BSSM files
+
+## SYNOPSIS
+
+*gthmkbssmfiles* output_path
+
+## DESCRIPTION
+
+Write hard coded BSSM files to output_path.
+
+## OPTIONS
+
+*-help*::
+  display help and exit
+
+*-version*::
+  display version information and exit
+

debian/man_src/gthsplit.1.adoc

+# gthsplit(1)
+
+## NAME
+
+gthsplit - split GenomeThreader output files
+
+## SYNOPSIS
+
+*gthsplit*  -alignmentscore | -coverage [option ...] [file ...]
+
+## DESCRIPTION
+
+Split GenomeThreader output files containing intermediate results.
+
+## OPTIONS
+
+*-alignmentscore*::
+  split according to the overall alignment score (scr)
+                   default: no
+
+*-coverage*::
+  split according to coverage (cov)
+                   default: no
+
+*-range*::
+  set the percentage range used to create the sets
+                   default: 5
+
+*-minalignmentscore*::
+  set the minimum alignment score for spliced alignments to be
+                   included into the set of spliced alignments
+                   default: 0.00
+
+*-maxalignmentscore*::
+  set the maximum alignment score for spliced alignments to be
+                   included into the set of spliced alignments
+                   default: 1.00
+
+*-mincoverage*::
+  set the minimum coverage for spliced alignments to be
+                   included into the set of spliced alignments
+                   default: 0.00
+
+*-maxcoverage*::
+  set the maximum coverage for spliced alignments to be
+                   included into the set of spliced alignments
+                   default: 9999.99
+
+*-v*::
+  be verbose
+                   default: no
+
+*-gzip*::
+  write gzip compressed output file(s)
+                   default: no
+
+*-bzip2*::
+  write bzip2 compressed output file(s)
+                   default: no
+
+*-force*::
+  force writing to split files
+                   default: no
+
+*-help*::
+  display help and exit
+
+*-version*::
+  display version information and exit
+

debian/patches/debian-gt-libs.patch

+Description: use Debian's GenomeTools
+Author: Sascha Steinbiss <satta@debian.org>
 --- a/Makefile
 +++ b/Makefile
 @@ -15,19 +15,17 @@

debian/patches/gt-path-fix.patch

+Description: use Debian's gt path
+Author: Sascha Steinbiss <satta@debian.org>
 --- a/testsuite/gthbssmtrain_include.rb
 +++ b/testsuite/gthbssmtrain_include.rb
 @@ -37,7 +37,7 @@

debian/patches/hardening.patch

+Description: Enable full hardening
+Author: Sascha Steinbiss <satta@debian.org>
+--- a/Makefile
++++ b/Makefile
+@@ -229,7 +229,7 @@
+ $(1): $(2)
+ 	@echo "[link $$(@F)]"
+ 	@test -d $$(@D) || mkdir -p $$(@D)
+-	$$(CC) $$(LDFLAGS) $$(GTH_LDFLAGS) $$(filter-out $$(OVERRIDELIBS),$$^) \
++	$$(CC) $$(CPPFLAGS) $$(LDFLAGS) $$(GTH_LDFLAGS) $$(filter-out $$(OVERRIDELIBS),$$^) \
+ 	  $$(filter-out $$(patsubst lib%.a,-l%,$$(notdir $$(OVERRIDELIBS))),\
+ 	  $$(EXP_LDLIBS)) $$(OVERRIDELIBS) -o $$@
+ endef
+@@ -319,7 +319,7 @@
+ $(1): $(2)
+ 	@echo "[compile $$(@F)]"
+ 	@test -d $$(@D) || mkdir -p $$(@D)
+-	$$(CC) -c $$< -o $$@ $$(EXP_CPPFLAGS) $$(GTH_CPPFLAGS) $$(EXP_CFLAGS) \
++	$$(CC) $$(CPPFLAGS) -c $$< -o $$@ $$(EXP_CPPFLAGS) $$(GTH_CPPFLAGS) $$(EXP_CFLAGS) \
+ 	  $$(GTH_CFLAGS) $(3)
+ 	$$(CC) -c $$< -o $$(@:.o=.d) $$(EXP_CPPFLAGS) $$(GTH_CPPFLAGS) \
+         $(3) -MM -MP -MT $$@

debian/patches/series

 debian-gt-libs.patch
 gt-path-fix.patch
+hardening.patch