[med-svn] [Git][med-team/hilive][master] 7 commits: Team upload.
Andreas Tille (@tille)
gitlab at salsa.debian.org
Mon Apr 27 15:53:25 BST 2026
Andreas Tille pushed to branch master at Debian Med / hilive
Commits:
e4e1a950 by Enrico Seiler at 2024-11-26T17:43:02+01:00
Team upload.
* Team upload.
* d/control: Experimental rebuild using the 3rd release candidate of
SeqAn 2.5.0
- - - - -
2f2cec9f by Enrico Seiler at 2024-11-26T17:50:44+01:00
Added patch for the explicit seqan2 namespace.
- - - - -
adbe5662 by Enrico Seiler at 2024-11-26T17:58:17+01:00
salsa ci: added
- - - - -
ca97c907 by Enrico Seiler at 2024-11-26T17:58:32+01:00
ready for uploading to experimental
- - - - -
93621631 by Andreas Tille at 2026-04-27T16:07:31+02:00
Drop libboost-system-dev from Build-Depends Closes: #1134916
- - - - -
0fbcf085 by Andreas Tille at 2026-04-27T16:12:19+02:00
No version restriction on libseqan2-dev
- - - - -
02487b0f by Andreas Tille at 2026-04-27T16:53:12+02:00
Do not try to use component system from Boost which was removed in version 1.90 Closes: #1134916
- - - - -
10 changed files:
- debian/changelog
- debian/control
- + debian/patches/0005-Upgrade-to-SeqAn-2.5.0.patch
- + debian/patches/0006-boost1.90.patch
- debian/patches/do_not_set_rpath.patch
- debian/patches/remove_march_native.patch
- debian/patches/series
- debian/patches/use_FindSeQan.patch
- debian/patches/use_dynamic_linking.patch
- + debian/salsa-ci.yml
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,23 @@
+hilive (2.0a-6) UNRELEASED; urgency=medium
+
+ * Drop libboost-system-dev from Build-Depends
+ Closes: #1134916
+ * No version restriction on libseqan2-dev
+ * Do not try to use component system from Boost which was removed
+ in version 1.90
+ Closes: #1134916
+
+ -- Andreas Tille <tille at debian.org> Mon, 27 Apr 2026 16:04:32 +0200
+
+hilive (2.0a-5) experimental; urgency=medium
+
+ * Team upload.
+ * d/control: Experimental rebuild using the 3rd release candidate of
+ SeqAn 2.5.0
+ * Added patch for the explicit seqan2 namespace.
+
+ -- Enrico Seiler <enrico.seiler.debian at outlook.com> Tue, 26 Nov 2024 17:58:24 +0100
+
hilive (2.0a-4) unstable; urgency=medium
* Team upload
=====================================
debian/control
=====================================
@@ -5,7 +5,6 @@ Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
cmake,
- libboost-system-dev,
libboost-filesystem-dev,
libboost-iostreams-dev,
libboost-program-options-dev,
=====================================
debian/patches/0005-Upgrade-to-SeqAn-2.5.0.patch
=====================================
@@ -0,0 +1,595 @@
+From: Enrico Seiler <enrico.seiler.debian at outlook.com>
+Date: Tue, 26 Nov 2024 17:45:08 +0100
+Subject: Upgrade to SeqAn 2.5.0.
+
+---
+ CMakeLists.txt | 2 +-
+ lib/alnout.cpp | 36 ++++++++++++++++++------------------
+ lib/alnout.h | 34 +++++++++++++++++-----------------
+ lib/alnread.cpp | 32 ++++++++++++++++----------------
+ lib/alnread.h | 4 ++--
+ lib/kindex.cpp | 22 +++++++++++-----------
+ lib/kindex.h | 10 +++++-----
+ lib/tools.cpp | 12 ++++++------
+ lib/tools.h | 2 +-
+ lib/tools_static.h | 2 +-
+ 10 files changed, 78 insertions(+), 78 deletions(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index aea27d4..7e06a9a 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -10,7 +10,7 @@ project( HiLive VERSION 2.0 LANGUAGES CXX )
+ ###################
+
+ # Set CXX Standard
+-set( CMAKE_CXX_STANDARD 14 )
++set( CMAKE_CXX_STANDARD 17 )
+ set( CMAKE_CXX_SANDARD_REQUIRED ON )
+ set( CMAKE_CXX_EXTENSIONS OFF )
+
+diff --git a/lib/alnout.cpp b/lib/alnout.cpp
+index f582e1e..169bce1 100755
+--- a/lib/alnout.cpp
++++ b/lib/alnout.cpp
+@@ -47,7 +47,7 @@ void AlnOut::init() {
+ bfos.set_context(idx->getSeqNames(), idx->getSeqLengths());
+
+ // Init the header (the same object can be used for all output streams)
+- seqan::BamHeader header = getBamHeader();
++ seqan2::BamHeader header = getBamHeader();
+
+ // Init output stream for each barcode (plus undetermined if keep_all_barcodes is set)
+ for ( unsigned barcode=0; barcode < (barcodes.size() + 1); barcode ++) {
+@@ -292,7 +292,7 @@ void AlnOut::__write_tile_to_bam__ ( Task t ) {
+ mateAlignments.push_back(e->get_alignment());
+ }
+
+- std::vector<std::vector<seqan::BamAlignmentRecord>> mateRecords(mateAlignments.size(), std::vector<seqan::BamAlignmentRecord>(0));
++ std::vector<std::vector<seqan2::BamAlignmentRecord>> mateRecords(mateAlignments.size(), std::vector<seqan2::BamAlignmentRecord>(0));
+
+ // if the filter file is available and the filter flag is 0 then skip
+ if (filters.size() != 0 && filters.next() == false)
+@@ -333,7 +333,7 @@ void AlnOut::__write_tile_to_bam__ ( Task t ) {
+ mateAlignments[mateAlignmentIndex]->cycle -= 1;
+
+ // Init record with information about the read
+- seqan::BamAlignmentRecord mate_record;
++ seqan2::BamAlignmentRecord mate_record;
+ mate_record.qName = readname.str();
+ mate_record.flag = 0;
+
+@@ -413,7 +413,7 @@ void AlnOut::__write_tile_to_bam__ ( Task t ) {
+ }
+
+ // get CIGAR-String
+- seqan::String<seqan::CigarElement<> > cigar = (*it)->returnSeqanCigarString();
++ seqan2::String<seqan2::CigarElement<> > cigar = (*it)->returnSeqanCigarString();
+
+ // Get NM:i value
+ unsigned nm = (*it)->get_nm();
+@@ -425,7 +425,7 @@ void AlnOut::__write_tile_to_bam__ ( Task t ) {
+ unsigned deletionSum = 0;
+ unsigned supposed_cigar_length = mateCycles[mateAlignmentIndex];
+
+- for (seqan::Iterator<seqan::String<seqan::CigarElement<> > >::Type elem = seqan::begin(cigar); elem != end(cigar); ++elem) {
++ for (seqan2::Iterator<seqan2::String<seqan2::CigarElement<> > >::Type elem = seqan2::begin(cigar); elem != end(cigar); ++elem) {
+ if ((elem->operation == 'M') || (elem->operation == 'I') || (elem->operation == 'S') || (elem->operation == '=') || (elem->operation == 'X'))
+ cigarElemSum += elem->count;
+
+@@ -464,7 +464,7 @@ void AlnOut::__write_tile_to_bam__ ( Task t ) {
+ goto nextmate;
+ }
+
+- seqan::BamAlignmentRecord record = mate_record;
++ seqan2::BamAlignmentRecord record = mate_record;
+
+ record.rID = CountType(p->gid / 2);
+
+@@ -485,40 +485,40 @@ void AlnOut::__write_tile_to_bam__ ( Task t ) {
+
+ record.cigar = cigar;
+ if ( idx->isReverse(p->gid) )
+- seqan::reverse(record.cigar);
++ seqan2::reverse(record.cigar);
+
+ if ( printedMateAlignments > 0 ) { // if current seed is secondary alignment
+ record.flag = addSAMFlag(record.flag, SAMFlag::SEC_ALIGNMENT);
+- seqan::clear(record.seq);
+- seqan::clear(record.qual);
++ seqan2::clear(record.seq);
++ seqan2::clear(record.qual);
+ }
+
+ if ( idx->isReverse(p->gid) ) { // if read matched reverse complementary
+- seqan::reverseComplement(record.seq);
+- seqan::reverse(record.qual);
++ seqan2::reverseComplement(record.seq);
++ seqan2::reverse(record.qual);
+ record.flag = addSAMFlag(record.flag, SAMFlag::SEQ_RC);
+ }
+
+ // Dictionary for additional SAM tags
+- seqan::BamTagsDict dict;
++ seqan2::BamTagsDict dict;
+
+ // Alignment Score
+- seqan::appendTagValue(dict, "AS", curr_seed_score);
++ seqan2::appendTagValue(dict, "AS", curr_seed_score);
+
+ // Barcode sequence
+ if (barcode!="")
+- seqan::appendTagValue(dict, "BC", barcode);
++ seqan2::appendTagValue(dict, "BC", barcode);
+
+ // Number of mismatches
+- seqan::appendTagValue(dict, "NM", nm);
++ seqan2::appendTagValue(dict, "NM", nm);
+
+ // MD:Z string
+ std::string mdz = (*it)->getMDZString();
+ if ( idx->isReverse(p->gid))
+ mdz = reverse_mdz(mdz);
+- seqan::appendTagValue(dict, "MD", mdz);
++ seqan2::appendTagValue(dict, "MD", mdz);
+
+- record.tags = seqan::host(dict);
++ record.tags = seqan2::host(dict);
+
+ // fill records list
+ mateRecords[mateAlignmentIndex].push_back(record);
+@@ -561,7 +561,7 @@ void AlnOut::__write_tile_to_bam__ ( Task t ) {
+ return;
+ }
+
+-void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords ) {
++void AlnOut::setMateSAMFlags( std::vector<std::vector<seqan2::BamAlignmentRecord>> & mateRecords ) {
+ for ( CountType i=0; i<mateRecords.size(); i++ ) {
+
+ // Stop if not paired
+diff --git a/lib/alnout.h b/lib/alnout.h
+index 4723925..eaad85c 100644
+--- a/lib/alnout.h
++++ b/lib/alnout.h
+@@ -20,7 +20,7 @@ struct Atomic_bfo {
+ private:
+
+ /** The BamFileOut stream.*/
+- seqan::BamFileOut bfo;
++ seqan2::BamFileOut bfo;
+
+ /** The atomic flag to perform a spinlock while writing.*/
+ std::atomic_flag flag = ATOMIC_FLAG_INIT;
+@@ -55,7 +55,7 @@ public:
+ * Set the context of the BamFileOut stream.
+ * @param context The new context.
+ */
+- void setContext ( seqan::BamIOContext<seqan::StringSet<seqan::CharString> > & context ) {
++ void setContext ( seqan2::BamIOContext<seqan2::StringSet<seqan2::CharString> > & context ) {
+ bfo.context = context;
+ }
+
+@@ -63,22 +63,22 @@ public:
+ * Write the header to the output file.
+ * @param header The header for the output file.
+ */
+- void writeHeader ( seqan::BamHeader & header ) {
+- seqan::writeHeader( bfo, header );
++ void writeHeader ( seqan2::BamHeader & header ) {
++ seqan2::writeHeader( bfo, header );
+ }
+
+ /**
+ * Write records to the output file in a "thread-safe" manner.
+ * @param records Reference to a vector containing a set of records.
+ */
+- void writeRecords ( std::vector<seqan::BamAlignmentRecord> & records ) {
++ void writeRecords ( std::vector<seqan2::BamAlignmentRecord> & records ) {
+
+ if ( records.size() == 0 )
+ return;
+
+ lock();
+
+- seqan::writeRecords(bfo, records);
++ seqan2::writeRecords(bfo, records);
+
+ unlock();
+
+@@ -88,7 +88,7 @@ public:
+ * Write records to the output file in a "thread-safe" manner.
+ * @param records Reference to a vector containing an other vector of records.
+ */
+- void writeRecords ( std::vector<std::vector<seqan::BamAlignmentRecord>> & records ) {
++ void writeRecords ( std::vector<std::vector<seqan2::BamAlignmentRecord>> & records ) {
+
+ if ( records.size() == 0 )
+ return;
+@@ -96,7 +96,7 @@ public:
+ lock();
+
+ for ( auto & subvector : records)
+- seqan::writeRecords(bfo, subvector);
++ seqan2::writeRecords(bfo, subvector);
+
+ unlock();
+
+@@ -115,9 +115,9 @@ class BamFileOutDeque {
+ std::deque<Atomic_bfo> bfos;
+
+ /** All fields needed for the context of the BamFileOut streams. */
+- seqan::BamIOContext<seqan::StringSet<seqan::CharString> > context;
+- seqan::StringSet<seqan::CharString> refNames;
+- seqan::NameStoreCache<seqan::StringSet<seqan::CharString> > refNamesCache;
++ seqan2::BamIOContext<seqan2::StringSet<seqan2::CharString> > context;
++ seqan2::StringSet<seqan2::CharString> refNames;
++ seqan2::NameStoreCache<seqan2::StringSet<seqan2::CharString> > refNamesCache;
+
+ public:
+
+@@ -127,12 +127,12 @@ public:
+ * @param seq_length Lengths of all sequences in the database
+ */
+ void set_context(std::vector<std::string> & seq_names, std::vector<uint32_t> & seq_lengths) {
+- seqan::NameStoreCache<seqan::StringSet<seqan::CharString> > rnc(refNames);
++ seqan2::NameStoreCache<seqan2::StringSet<seqan2::CharString> > rnc(refNames);
+ refNamesCache = rnc;
+- seqan::BamIOContext<seqan::StringSet<seqan::CharString> > cxt(refNames, refNamesCache);
++ seqan2::BamIOContext<seqan2::StringSet<seqan2::CharString> > cxt(refNames, refNamesCache);
+ context = cxt;
+- seqan::contigNames(context) = seq_names;
+- seqan::contigLengths(context) = seq_lengths;
++ seqan2::contigNames(context) = seq_names;
++ seqan2::contigLengths(context) = seq_lengths;
+ }
+
+ /**
+@@ -246,7 +246,7 @@ private:
+ bool add_task( Task t, ItemStatus status );
+
+ // TODO: documentation
+- void findPairs( std::vector<std::vector<seqan::BamAlignmentRecord>> & mateRecords );
++ void findPairs( std::vector<std::vector<seqan2::BamAlignmentRecord>> & mateRecords );
+
+ /**
+ * Set the SAM fields according to the information about the other mates.
+@@ -254,7 +254,7 @@ private:
+ * For the last mate, refer to the first mate (as it is done for paired end data)
+ * @param reference to a vecor of vectors for SAM records of each mate.
+ */
+- void setMateSAMFlags( std::vector<std::vector<seqan::BamAlignmentRecord>> & records );
++ void setMateSAMFlags( std::vector<std::vector<seqan2::BamAlignmentRecord>> & records );
+
+ /**
+ * Create a temporary align file that is sorted by score.
+diff --git a/lib/alnread.cpp b/lib/alnread.cpp
+index 6c3fbae..920e0a9 100755
+--- a/lib/alnread.cpp
++++ b/lib/alnread.cpp
+@@ -1,13 +1,13 @@
+ #include "alnread.h"
+
+
+-seqan::String<seqan::CigarElement<> > Seed::returnSeqanCigarString() const {
++seqan2::String<seqan2::CigarElement<> > Seed::returnSeqanCigarString() const {
+
+ bool extended_cigar = globalAlignmentSettings.get_extended_cigar();
+
+- typedef seqan::String<seqan::CigarElement<> > TSeqanCigarString;
++ typedef seqan2::String<seqan2::CigarElement<> > TSeqanCigarString;
+ TSeqanCigarString seqanCigarString;
+- seqan::CigarElement<> cigarElem;
++ seqan2::CigarElement<> cigarElem;
+
+ for (CigarVector::const_iterator it = cigar_data.begin(); it != cigar_data.end(); ++it) {
+
+@@ -15,7 +15,7 @@ seqan::String<seqan::CigarElement<> > Seed::returnSeqanCigarString() const {
+ if (it == cigar_data.begin() && (*it).operation==NO_MATCH) {
+ cigarElem.operation='S';
+ cigarElem.count=(*it).length;
+- seqan::appendValue(seqanCigarString, cigarElem);
++ seqan2::appendValue(seqanCigarString, cigarElem);
+ continue;
+ }
+
+@@ -23,7 +23,7 @@ seqan::String<seqan::CigarElement<> > Seed::returnSeqanCigarString() const {
+ if ((*it).operation==NO_MATCH) {
+ cigarElem.operation= extended_cigar ? 'X' : 'M';
+ cigarElem.count=(*it).length;
+- seqan::appendValue(seqanCigarString, cigarElem);
++ seqan2::appendValue(seqanCigarString, cigarElem);
+ continue;
+ }
+
+@@ -31,7 +31,7 @@ seqan::String<seqan::CigarElement<> > Seed::returnSeqanCigarString() const {
+ else if((*it).operation==DELETION) {
+ cigarElem.operation='D';
+ cigarElem.count=(*it).length;
+- seqan::appendValue(seqanCigarString, cigarElem);
++ seqan2::appendValue(seqanCigarString, cigarElem);
+ continue;
+ }
+
+@@ -39,7 +39,7 @@ seqan::String<seqan::CigarElement<> > Seed::returnSeqanCigarString() const {
+ else if((*it).operation==INSERTION) {
+ cigarElem.operation='I';
+ cigarElem.count=(*it).length;
+- seqan::appendValue(seqanCigarString, cigarElem);
++ seqan2::appendValue(seqanCigarString, cigarElem);
+ continue;
+ }
+
+@@ -47,7 +47,7 @@ seqan::String<seqan::CigarElement<> > Seed::returnSeqanCigarString() const {
+ else {
+ cigarElem.operation= extended_cigar ? '=' : 'M';
+ cigarElem.count=(*it).length;
+- seqan::appendValue(seqanCigarString, cigarElem);
++ seqan2::appendValue(seqanCigarString, cigarElem);
+ continue;
+
+ }
+@@ -395,8 +395,8 @@ std::vector<GenomePosType> Seed::getPositions( CountType firstPosition, CountTyp
+ std::vector<GenomePosType> position_list;
+
+ // Get occurences
+- auto positions = seqan::getOccurrences(it);
+- CountType sub_positions = seqan::length(positions);
++ auto positions = seqan2::getOccurrences(it);
++ CountType sub_positions = seqan2::length(positions);
+ position_list.reserve( std::min ( seed_positions, sub_positions ) );
+
+ // Put positions into the return list
+@@ -656,7 +656,7 @@ void ReadAlignment::extendSeed(char base, USeed origin, SeedVec & newSeeds){
+ {
+ // Handle matching nucleotide first (this should be the default case)
+ FMTopDownIterator it(idx->idx, origin->vDesc);
+- if ( seqan::goDown(it, seqan::DnaString(base)) ) {
++ if ( seqan2::goDown(it, seqan2::DnaString(base)) ) {
+ getMatchSeeds( tbr, tbr, it, origin, newSeeds );
+ handled_range += (it.vDesc.range.i2 - it.vDesc.range.i1);
+ }
+@@ -683,7 +683,7 @@ void ReadAlignment::extendSeed(char base, USeed origin, SeedVec & newSeeds){
+
+ FMTopDownIterator it(idx->idx, origin->vDesc);
+
+- if ( seqan::goDown(it, seqan::DnaString(index_base)) ) {
++ if ( seqan2::goDown(it, seqan2::DnaString(index_base)) ) {
+
+ // Handle no_match
+ getMatchSeeds( tbr, index_base, it, origin, newSeeds );
+@@ -851,7 +851,7 @@ void ReadAlignment::recursive_goDown(CountType base_repr, USeed origin, SeedVec
+ FMTopDownIterator it(idx->idx, origin->vDesc);
+
+ // Only consider paths existing in the index
+- if ( goDown(it, seqan::DnaString(revtwobit_repr( base_repr )))) {
++ if ( goDown(it, seqan2::DnaString(revtwobit_repr( base_repr )))) {
+
+ // copy data from origin seed
+ USeed s (new Seed);
+@@ -894,7 +894,7 @@ void ReadAlignment::recursive_goDown(CountType base_repr, USeed origin, SeedVec
+ FMTopDownIterator it(idx->idx, origin->vDesc);
+
+ // Only consider paths existing in the index
+- if ( goDown(it, seqan::DnaString(revtwobit_repr(b)))) {
++ if ( goDown(it, seqan2::DnaString(revtwobit_repr(b)))) {
+
+ // copy data from origin seed
+ USeed s (new Seed);
+@@ -926,7 +926,7 @@ void ReadAlignment::createSeeds(SeedVec & newSeeds) {
+ std::string anchor_seq = getSequenceString().substr( sequenceLen - globalAlignmentSettings.get_anchor_length(), globalAlignmentSettings.get_anchor_length());
+
+ FMTopDownIterator it(idx->idx);
+- if ( seqan::goDown(it, seqan::Dna5String(anchor_seq)) ) {
++ if ( seqan2::goDown(it, seqan2::Dna5String(anchor_seq)) ) {
+ USeed seed ( new Seed() );
+ seed->max_as = max_as;
+ if ( cycle != globalAlignmentSettings.get_anchor_length() )
+@@ -1189,7 +1189,7 @@ std::vector<uint8_t> ReadAlignment::getMAPQs() const {
+ return mapqs;
+ }
+
+-void ReadAlignment::addReadInfoToRecord(seqan::BamAlignmentRecord & record) const {
++void ReadAlignment::addReadInfoToRecord(seqan2::BamAlignmentRecord & record) const {
+ record.seq = getSequenceString();
+ record.qual = getQualityString();
+ }
+diff --git a/lib/alnread.h b/lib/alnread.h
+index f800b80..9ed4305 100644
+--- a/lib/alnread.h
++++ b/lib/alnread.h
+@@ -39,7 +39,7 @@ struct Seed {
+ * @return CIGAR string in SeqAn format
+ * TODO: give extended CIGAR information as a parameter instead of inside the function.
+ */
+- seqan::String<seqan::CigarElement<> > returnSeqanCigarString() const;
++ seqan2::String<seqan2::CigarElement<> > returnSeqanCigarString() const;
+
+ /**
+ * Get the alignment score of a seed (AS:i).
+@@ -407,7 +407,7 @@ public:
+ */
+ std::vector<uint8_t> getMAPQs() const;
+
+- void addReadInfoToRecord(seqan::BamAlignmentRecord & record) const;
++ void addReadInfoToRecord(seqan2::BamAlignmentRecord & record) const;
+
+ }; // END class ReadAlignment
+
+diff --git a/lib/kindex.cpp b/lib/kindex.cpp
+index 22ca65c..6be1b89 100644
+--- a/lib/kindex.cpp
++++ b/lib/kindex.cpp
+@@ -23,20 +23,20 @@ int KixBuild::create_index( const std::string &fname, const std::string &iname,
+ }
+
+ // modify sequences for index building (reverse and add reverse complement)
+- seqan::StringSet<seqan::DnaString> all_seqs;
++ seqan2::StringSet<seqan2::DnaString> all_seqs;
+
+ for(uint16_t i = 0; i < length(seqs); i++) {
+- seqan::ModifiedString<seqan::DnaString, seqan::ModReverse> rev(seqs[i]);
+- seqan::appendValue(all_seqs, rev);
+- seqan::complement(seqs[i]);
+- seqan::appendValue(all_seqs, seqs[i]);
++ seqan2::ModifiedString<seqan2::DnaString, seqan2::ModReverse> rev(seqs[i]);
++ seqan2::appendValue(all_seqs, rev);
++ seqan2::complement(seqs[i]);
++ seqan2::appendValue(all_seqs, seqs[i]);
+ }
+
+ // Define the index
+ FMIndex idx(all_seqs);
+
+ // Force the index to be created
+- if( ! seqan::indexCreate(idx) )
++ if( ! seqan2::indexCreate(idx) )
+ return 4;
+
+ // Save the index to file
+@@ -61,7 +61,7 @@ int KixBuild::add_fasta(const std::string &fname, bool convert_spaces, bool trim
+ std::string line; // current line of fasta file
+ std::string seq_name; // name of the current sequence
+ bool startNewSequence = false; // true if last line was a header / new sequence begins
+- seqan::DnaString newSeq = ""; // current DNA sequence
++ seqan2::DnaString newSeq = ""; // current DNA sequence
+
+ while(getline(infile, line)) {
+
+@@ -79,7 +79,7 @@ int KixBuild::add_fasta(const std::string &fname, bool convert_spaces, bool trim
+
+ // add last sequence to sequence vector (if exist)
+ if ( newSeq != "" ) {
+- seqan::appendValue(seqs, newSeq);
++ seqan2::appendValue(seqs, newSeq);
+ }
+
+ // trim the header (remove leading and trailing whitespaces)
+@@ -125,7 +125,7 @@ int KixBuild::add_fasta(const std::string &fname, bool convert_spaces, bool trim
+
+ // append the last sequence to the StringSet
+ if ( newSeq != "" ) {
+- seqan::appendValue(seqs, newSeq);
++ seqan2::appendValue(seqs, newSeq);
+ }
+
+ return seq_lengths.size();
+@@ -134,7 +134,7 @@ int KixBuild::add_fasta(const std::string &fname, bool convert_spaces, bool trim
+
+ int KixBuild::save_fmindex( FMIndex & idx, const std::string &iname ) {
+ const char * filename = iname.c_str();
+- return seqan::save(idx, filename);
++ return seqan2::save(idx, filename);
+ }
+
+ int KixBuild::save_metadata( const std::string &iname ) {
+@@ -227,7 +227,7 @@ int KixRun::load_fmindex( std::string index_name ) {
+
+ const char * filename = index_name.c_str();
+
+- if ( seqan::open(idx, filename) != 1 ) // function returns 1 on success
++ if ( seqan2::open(idx, filename) != 1 ) // function returns 1 on success
+ return 1;
+ return 0;
+
+diff --git a/lib/kindex.h b/lib/kindex.h
+index 5742035..c8f8283 100644
+--- a/lib/kindex.h
++++ b/lib/kindex.h
+@@ -12,22 +12,22 @@
+ /**
+ * FM-Index Config.
+ */
+-typedef seqan::FastFMIndexConfig<void, uint64_t,2 ,1> FMIConfig;
++typedef seqan2::FastFMIndexConfig<void, uint64_t,2 ,1> FMIConfig;
+
+ /**
+ * FM-Index data type.
+ */
+-typedef seqan::Index<seqan::StringSet<seqan::DnaString>, seqan::FMIndex<void, FMIConfig> > FMIndex;
++typedef seqan2::Index<seqan2::StringSet<seqan2::DnaString>, seqan2::FMIndex<void, FMIConfig> > FMIndex;
+
+ /**
+ * Iterator to go through the FM index structure.
+ */
+-typedef seqan::Iterator<FMIndex, seqan::TopDown<> >::Type FMTopDownIterator;
++typedef seqan2::Iterator<FMIndex, seqan2::TopDown<> >::Type FMTopDownIterator;
+
+ /**
+ * Data type to find a store a node in the FM index.
+ */
+-typedef seqan::Iter<FMIndex,seqan::VSTree<seqan::TopDown<seqan::Preorder>>>::TVertexDesc FMVertexDescriptor;
++typedef seqan2::Iter<FMIndex,seqan2::VSTree<seqan2::TopDown<seqan2::Preorder>>>::TVertexDesc FMVertexDescriptor;
+
+ inline bool operator==(const FMVertexDescriptor l, FMVertexDescriptor r) {
+ return l.range == r.range;
+@@ -76,7 +76,7 @@ class KixBuild {
+ std::vector<uint32_t> seq_lengths;
+
+ /** Sequences in the index. */
+- seqan::StringSet<seqan::DnaString> seqs;
++ seqan2::StringSet<seqan2::DnaString> seqs;
+
+ private:
+
+diff --git a/lib/tools.cpp b/lib/tools.cpp
+index f5120f3..bb9595d 100644
+--- a/lib/tools.cpp
++++ b/lib/tools.cpp
+@@ -4,25 +4,25 @@
+ ////////// SAM/BAM output //////////
+ ////////////////////////////////////
+
+-seqan::BamHeader getBamHeader() {
++seqan2::BamHeader getBamHeader() {
+ std::stringstream ss;
+ ss.str(std::string());
+ ss << HiLive_VERSION_MAJOR << "." << HiLive_VERSION_MINOR;
+
+- seqan::BamHeader header;
++ seqan2::BamHeader header;
+ resize(header, 2);
+
+ // @HD header.
+- seqan::resize(header[0].tags, 2);
+- header[0].type = seqan::BAM_HEADER_FIRST;
++ seqan2::resize(header[0].tags, 2);
++ header[0].type = seqan2::BAM_HEADER_FIRST;
+ header[0].tags[0].i1 = "VN";
+ header[0].tags[0].i2 = "1.5";
+ header[0].tags[1].i1 = "GO";
+ header[0].tags[1].i2 = "query";
+
+ // @PG header.
+- seqan::resize(header[1].tags, 3);
+- header[1].type = seqan::BAM_HEADER_PROGRAM;
++ seqan2::resize(header[1].tags, 3);
++ header[1].type = seqan2::BAM_HEADER_PROGRAM;
+ header[1].tags[0].i1 = "ID";
+ header[1].tags[0].i2 = "hilive";
+ header[1].tags[1].i1 = "PN";
+diff --git a/lib/tools.h b/lib/tools.h
+index 6f4167f..b9114c2 100644
+--- a/lib/tools.h
++++ b/lib/tools.h
+@@ -134,7 +134,7 @@ inline uint16_t getMateCycle( uint16_t mate_number, uint16_t seq_cycle ) {
+ * @return The BAM header.
+ * @author Tobias Loka
+ */
+-seqan::BamHeader getBamHeader();
++seqan2::BamHeader getBamHeader();
+
+ /**
+ * Name of a temporary SAM/BAM file (for the time it is written).
+diff --git a/lib/tools_static.h b/lib/tools_static.h
+index 99d084a..d353c88 100644
+--- a/lib/tools_static.h
++++ b/lib/tools_static.h
+@@ -36,7 +36,7 @@ inline bool gp_compare (GenomePosType i,GenomePosType j) {
+ * @param r Second record.
+ * @return true, if l has a lower positions than r.
+ */
+-inline bool compare_records_by_pos(const seqan::BamAlignmentRecord & l, const seqan::BamAlignmentRecord & r) {
++inline bool compare_records_by_pos(const seqan2::BamAlignmentRecord & l, const seqan2::BamAlignmentRecord & r) {
+ if ( l.rID == r.rID )
+ return l.beginPos < r.beginPos;
+ return l.rID < r.rID;
=====================================
debian/patches/0006-boost1.90.patch
=====================================
@@ -0,0 +1,16 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2027-04-27
+Bug-Debian: https://bugs.debian.org/1134916
+Description: Boost 1.90 has no component system any more
+
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -78,7 +78,7 @@ endif()
+ set(Boost_USE_STATIC_LIBS OFF)
+ set(Boost_USE_MULTITHREADED ON)
+ set(Boost_USE_STATIC_RUNTIME OFF)
+-find_package( Boost COMPONENTS system filesystem program_options iostreams REQUIRED )
++find_package( Boost COMPONENTS filesystem program_options iostreams REQUIRED )
+ include_directories( ${Boost_INCLUDE_DIR} )
+
+ # ZLIB
=====================================
debian/patches/do_not_set_rpath.patch
=====================================
@@ -1,10 +1,18 @@
-Author: Andreas Tille <tille at debian.org>
+From: Andreas Tille <tille at debian.org>
+Date: Fri, 29 Jul 2016 14:17:48 +0200
+Subject: Do not set rpath
+
Last-Update: Thu, 28 Jul 2016 15:13:14 +0200
-Description: Do not set rpath
- Unfortunately this does not work and chrpath needs to be used.
- .
- Any hint to do this properly is welcome.
+Unfortunately this does not work and chrpath needs to be used.
+
+Any hint to do this properly is welcome.
+---
+ CMakeLists.txt | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index af79c36..96e4782 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -120,6 +120,7 @@ foreach (x ${LIB_NAMES})
=====================================
debian/patches/remove_march_native.patch
=====================================
@@ -1,11 +1,19 @@
-Description: -march=native must not be used for distribution packages
- The resulting binaries may be dependent on features of the build machine.
-Author: Juhani Numminen <juhaninumminen0 at gmail.com>
+From: Juhani Numminen <juhaninumminen0 at gmail.com>
+Date: Thu, 16 Jan 2020 11:56:35 +0200
+Subject: -march=native must not be used for distribution packages
+
Last-Update: 2020-01-16
+The resulting binaries may be dependent on features of the build machine.
+---
+ CMakeLists.txt | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index e342f04..aea27d4 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-@@ -53,7 +53,7 @@
+@@ -53,7 +53,7 @@ endif()
# SeqAn specific flags
if ( NOT CONDA )
=====================================
debian/patches/series
=====================================
@@ -2,3 +2,5 @@ do_not_set_rpath.patch
use_FindSeQan.patch
use_dynamic_linking.patch
remove_march_native.patch
+0005-Upgrade-to-SeqAn-2.5.0.patch
+0006-boost1.90.patch
=====================================
debian/patches/use_FindSeQan.patch
=====================================
@@ -1,9 +1,16 @@
-Description: remove forced cflags and set proper cmake module path
-Author: Gert Wollny <gw.fossdev at gmail.com>
+From: Gert Wollny <gw.fossdev at gmail.com>
+Date: Tue, 6 Dec 2016 07:46:25 +0000
+Subject: remove forced cflags and set proper cmake module path
+---
+ CMakeLists.txt | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 96e4782..70d17dc 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-@@ -94,8 +94,8 @@ set(CompressionLibs "${ZLIB_LIBRARIES};l
+@@ -94,8 +94,8 @@ set(CompressionLibs "${ZLIB_LIBRARIES};lz4")
# SEQAN
if ( SEQAN_PATH )
=====================================
debian/patches/use_dynamic_linking.patch
=====================================
@@ -1,7 +1,15 @@
-Author: Andreas Tille <tille at debian.org>
+From: Andreas Tille <tille at debian.org>
+Date: Mon, 7 Oct 2019 13:35:34 +0200
+Subject: Do not link statically;
+ -pthread option (otherwise its -lpthread which does not work)
+
Last-Update: Mon, 07 Oct 2019 11:02:50 +0200
-Description: Do not link statically; -pthread option (otherwise its -lpthread which does not work)
+---
+ CMakeLists.txt | 7 ++++---
+ 1 file changed, 4 insertions(+), 3 deletions(-)
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 70d17dc..e342f04 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -53,11 +53,12 @@ endif()
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,6 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/recipes/debian.yml
+
+reprotest:
+ allow_failure: true
View it on GitLab: https://salsa.debian.org/med-team/hilive/-/compare/a5660256847b402c5afaee69200f1fd4a77c3edd...02487b0ff72e60884ae3c61750ceb7ffb874e82a
--
View it on GitLab: https://salsa.debian.org/med-team/hilive/-/compare/a5660256847b402c5afaee69200f1fd4a77c3edd...02487b0ff72e60884ae3c61750ceb7ffb874e82a
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