LICENSE

@@ -17,6 +17,13 @@ with this program; if not, write to the Free Software Foundation, Inc.,
 
 -------------------------------------------------------------------------------
 
+SPAdes
+Genome assembler for single-cell and isolates data sets
+Version: see VERSION
+
+Developed in Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University.
+Developed in Algorithmic Biology Lab of St. Petersburg Academic University of the Russian Academy of Sciences.
+
 Current SPAdes contributors:
 
     Dmitry Antipov,
@@ -51,9 +58,10 @@ Also contributed:
     Irina Vasilinetc,
     Nikolay Vyahhi
 
-Contacts:
+Installation instructions and manual can be found on the website:
 http://cab.spbu.ru/software/spades/
-    spades.support@cab.spbu.ru
+
+Address for communication: spades.support@cab.spbu.ru
 
 References:
 

README

-SPAdes
-Genome assembler for single-cell and isolates data sets
-Version: see VERSION
-
-Developed in Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University.
-Developed in Algorithmic Biology Lab of St. Petersburg Academic University of the Russian Academy of Sciences.
-
-Current SPAdes contributors:
-
-    Dmitry Antipov,
-    Anton Bankevich,
-    Elena Bushmanova,
-    Vasisliy Ershov,
-    Yuriy Gorshkov,
-    Alexey Gurevich,
-    Anton Korobeynikov,
-    Sergey Nurk,
-    Andrey Prjibelski,
-    Ivan Tolstoganov,
-    Alla Lapidus and
-    Pavel Pevzner
-
-Also contributed:
-
-    Max Alekseyev,
-    Mikhail Dvorkin,
-    Alexander Kulikov,
-    Valery Lesin,
-    Dmitriy Meleshko,
-    Sergey Nikolenko,
-    Son Pham,
-    Alexey Pyshkin,
-    Yana Safonova,
-    Vladislav Saveliev,
-    Alexander Sirotkin,
-    Yakov Sirotkin,
-    Artem Tarasov,
-    Glenn Tesler,
-    Irina Vasilinetc,
-    Nikolay Vyahhi
-
-Installation instructions and manual can be found on the website:
-http://cab.spbu.ru/software/spades/
-
-Address for communication: spades.support@cab.spbu.ru
-
-References:
-
-Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A. Gurevich, Mikhail Dvorkin, Alexander S. Kulikov, Valery M. Lesin,
-Sergey I. Nikolenko, Son Pham, Andrey D. Prjibelski, Alexey V. Pyshkin, Alexander V. Sirotkin, Nikolay Vyahhi, Glenn Tesler,
-Max A. Alekseyev, and Pavel A. Pevzner. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing.
-Journal of Computational Biology 19(5) (2012), 455-477. doi:10.1089/cmb.2012.0021
-
-Sergey Nurk, Anton Bankevich, Dmitry Antipov, Alexey Gurevich, Anton Korobeynikov,
-Alla Lapidus, Andrey Prjibelsky, Alexey Pyshkin, Alexander Sirotkin,
-Yakov Sirotkin, Ramunas Stepanauskas, Jeffrey McLean, Roger Lasken,
-Scott Clingenpeel, Tanja Woyke, Glenn Tesler, Max Alekseyev, and Pavel Pevzner.
-Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads. Lecture Notes
-in Computer Science 7821 (2013), pp. 158-170. doi:10.1007/978-3-642-37195-0_13
-

VERSION

-3.12.0
+3.13.0

changelog.html

@@ -3,6 +3,18 @@
 
 <h2>SPAdes Genome Assembler changelog</h2>
 
+<h3>SPAdes 3.13.0, 11 October 2018</h3>
+
+<p>CHANGE: Switched to multi-k-mer mode in rnaSPAdes, k-mer values are detected automatically based on read length.</p>
+
+<p>CHANGE: Added manual as README.md in markdown format for github.</p>
+
+<p>FIX: Updated BWA and switched to RopeBWT, which allows to handle large graphs.</p>
+
+<p>FIX: Assert for path.length() > 0 in rnaSPAdes. </p>
+
+<p>FIX: CQF and k-mer counting. </p>
+
 <h3>SPAdes 3.12.0, 14 May 2018</h3>
 
 <p>NEW: Support for merged paired-end reads.</p>

configs/debruijn/diploid_mode.info

-mode diploid
-
-simp
-{
-	; bulge remover:
-	br
-	{
-		enabled false
-	}
-}
-
-amb_de {
-    enabled true
-}

configs/debruijn/log.properties

@@ -51,6 +51,7 @@ default=INFO
 #LoopDetectingPathExtender=DEBUG
 #SimpleExtender=DEBUG
 #ScaffoldingPathExtender=DEBUG
+#ScaffoldingExtensionChooser=DEBUG
 #CoordCoverageExtensionChooser=DEBUG
 #SimpleCoverageExtensionChooser=DEBUG
 #IdealInfoProvider=TRACE

configs/dipspades/config.info

-; base parameters ;
-bp {
-	K			        55;
-	use_multithreading	true;
-	max_threads		    16;
-	max_memory		    512;
-    ; size of buffer for each thread in MB, 0 for autodetection
-    read_buffer_size 0
-}
-
-; input-output params ;
-io {
-	haplocontigs	haplocontigs
-	log_filename 	log.properties
-	output_base		data/debruijn
-	output_dir		simulated_e.coli_100k
-	tmp_dir			dipspades_tmp/
-	saves   		data/debruijn
-}
-
-; run params ;
-rp {
-	entry_point	    dipspades
-    : entry_point   dipspades:heterozygosity_estimation
-    ; entry_point   dipspades:contig_graph_construction
-    ; entry_point   dipspades:polymorphic_br
-    ; entry_point   dipspades:dipspades
-    ; entry_point   dipspades:consensus_construction
-    ; entry_point   dipspades:haplotype_assembly
-	developer_mode	true
-}
-
-; polymorphic bulge remover config
-pbr {
-	enabled                         true
-	rel_bulge_length                .8      ; min(len1, len2) / max(len1, len2) >= rel_bulge_length
-                                                ; where len1, len2 - lengths of bulge sides
-	rel_bulge_align                 .5      ; editdist(seq1, seq2) / min(|seq1|, |seq2|) <= rel_bulge_align
-                                                ; where seq1, seq2 - sequences of bulge sides
-	paired_vert_abs_threshold       50      ;
-	paired_vert_rel_threshold       .15     ;
-	max_bulge_nucls_len             25000   ; maximal length (in nt number) of bulge sides
-	max_neigh_number                100     ; maximal number of neighs for bulge search
-	num_iters_lbr                   15      ; number of light bulge remover iterations
-}
-
-; consensus constructor config
-cc {
-	    enabled                         true
-        bulge_len_quantile              .95                             ; value of this quantile of bulge length histogram
-                                                                        ; is upper bound of bulge length in contigs
-        tails_lie_on_bulges             true                            ; tail has to lie on bulge side
-		estimate_tails					true
-        align_bulge_sides               true                            ; check bulge into paired haplocontigs for alignment
-        min_overlap_size                1500                            ; minimal allowable length of overlap (in nt)
-        min_lcs_size                    1500                            ; minimal allowable length of shared subsequence of
-                                                                        ; paired contigs (in nt)
-        max_loop_length                 500                             ; maximal length of loop that can ignored in remover red contigs
-}
-
-; haplotype_assembly
-ha {
-	ha_enabled                         true
-}

configs/dipspades/log.properties

-default=INFO
-
-#PolymorphicBulgeRemover=TRACE
-#BulgeSplitter=TRACE
-#SubpathSplitter=TRACE
-#ComplexBulgeGluer=TRACE
-#GluingVericesDefiner=TRACE
-#GluingVericesDefinerResults=TRACE
-#ConsensusContigsConstructor=TRACE
-#CloseGapsCorrector=TRACE
-#LoopBulgeDeletionCorrector=TRACE
-#CompositeMappingContig=TRACE
-#DiploidContigSeparator=TRACE
-#ContigLabelAllocator=TRACE
-#OverlappedContigsMap=TRACE
-#OverlapCorrector=TRACE
-#EqualSequencesGluer=TRACE
-
-#DeBruijnGraphConstructor=TRACE
-#PairedHandlerApplier=TRACE
-#QualityEdgeLocalityPrintingRH=TRACE
-#PairInfoAwareErroneousEdgeRemover=TRACE
-#QualityLoggingRemovalHandler=TRACE
-#MatePairTransformStat=TRACE
-#EditDistanceTrackingCallback=TRACE
-#RepeatResolver=TRACE
-#PairInfoImprover=TRACE
-#BulgeRemover=TRACE
-#AbstractConjugateGraph=TRACE
-#PathProcessor=TRACE
-#DistanceEstimationQualityStat=TRACE
-#Dijkstra=TRACE
-#AbstractGraph=TRACE
-#PathSetGraphConstructor=TRACE
-#NewExtendedSequenceMapper=TRACE
-#JumpingPairInfoChecker=TRACE

debian/changelog

+spades (3.13.0+dfsg-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+  * Upstream has removed dipspades
+
+ -- Andreas Tille <tille@debian.org>  Tue, 16 Oct 2018 20:45:36 +0200
+
 spades (3.12.0+dfsg-1) unstable; urgency=medium
 
   [ Andreas Tille ]

debian/createmanpages

@@ -5,6 +5,3 @@ mkdir -p $MANDIR
 help2man --no-info --no-discard-stderr \
          --name='SPAdes genome assembler' \
             --version-string="$VERSION" spades > $MANDIR/spades.1
-help2man --no-info --no-discard-stderr \
-         --name='genome assembler designed for diploid genomes with high heterozygosity rate' \
-            --version-string="$VERSION" dipspades > $MANDIR/dipspades.1

debian/doc-base.dipspades

-Document: dipspades
-Title: dipSPAdes Manual
-Author: Dmitry Antipov, Anton Bankevich, Alexey Gurevich, a.o.
-Abstract: dipSPAdes is a genome assembler designed specifically for diploid highly        
- polymorphic genomes based on SPAdes. It takes advantage of divergence between
- haplomes in repetitive genome regions to resolve them and construct longer
- contigs. dipSPAdes produces consensus contigs (representing a consensus of both
- haplomes for the orthologous regions) and performs haplotype assembly. Note
- that dipSPAdes can only benefit from high polymorphism rate (at least 0.4%).
- For the data with low polymorphism rate no improvement in terms of N50 vs
- consentional assemblers is expected.
-Section: Science/Biology
-
-Format: html
-Index: /usr/share/doc/spades/dipspades_manual.html
-Files: /usr/share/doc/spades/dipspades_manual.html

debian/docs

 *manual.html
-manual.md

debian/links

 usr/bin/spades  usr/bin/spades.py
 usr/bin/spades  usr/bin/spades
-usr/bin/spades  usr/bin/dipspades.py
-usr/bin/spades  usr/bin/dipspades
 usr/bin/spades  usr/bin/truspades.py
 usr/bin/spades  usr/bin/truspades
 usr/bin/spades  usr/bin/metaspades.py
@@ -12,7 +10,6 @@ usr/bin/spades  usr/bin/rnaspades.py
 usr/bin/spades  usr/bin/rnaspades
 usr/bin/bwa     usr/lib/spades/bin/spades-bwa
 usr/share/man/man1/spades.1.gz /usr/share/man/man1/spades.py.1.gz
-usr/share/man/man1/dipspades.1.gz /usr/share/man/man1/dipspades.py.1.gz
 usr/share/man/man1/truspades.1.gz /usr/share/man/man1/truspades.py.1.gz
 usr/share/man/man1/metaspades.1.gz /usr/share/man/man1/metaspades.py.1.gz
 usr/share/man/man1/plasmidspades.1.gz /usr/share/man/man1/plasmidspades.py.1.gz

debian/man_src/dipspades.1.adoc

-= dipspades(1)
-
-## NAME
-
-dipspades - diploid genome assembler
-
-## SYNOPSIS
-
-*dipspades* [options] -o <output_dir>
-
-## DESCRIPTION
-
-*dipspades* is the main executable for the **dipSPAdes** software, a genome
-assembler designed for diploid genomes with a high heterozygosity rate. It
-assembles genomic reads given to it and places the resulting assembly in
-<output_dir>.
-
-## OPTIONS
-
-### Basic options
-
-*-o* <output_dir>::
-   directory to store all the resulting files (required)
-
-*--iontorrent*::
-   this flag is required for IonTorrent data
-
-*--test*::
-   runs dipSPAdes on toy dataset
-
-*-h*/*--help*::
-   prints this usage message
-
-### Input data
-
-*--12* <filename>::
-   file with interlaced forward and reverse paired-end reads
-
-*-1* <filename>::
-   file with forward paired-end reads
-
-*-2* <filename>::
-   file with reverse paired-end reads
-
-*-s* <filename>::
-   file with unpaired reads
-
-*--pe<#>-12* <filename>::
-   file with interlaced reads for paired-end library number <#> (<#> = 1,2,3,4,5)
-
-*--pe<#>-1* <filename>::
-  file with forward reads for paired-end library number <#> (<#> = 1,2,3,4,5)
-*--pe<#>-2* <filename>::
-  file with reverse reads for paired-end library number <#> (<#> = 1,2,3,4,5)
-*--pe<#>-s* <filename>::
-  file with unpaired reads for paired-end library number <#> (<#> = 1,2,3,4,5)
-*--pe<#>-<or>*::
-   orientation of reads for paired-end library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
-*--s<#>* <filename>::
-  file with unpaired reads for single reads library number <#> (<#> = 1,2,3,4,5)
-*--mp<#>-12*  <filename>::
-   file with interlaced reads for mate-pair library number <#> (<#> = 1,2,3,4,5)
-*--mp<#>-1* <filename>::
-  file with forward reads for mate-pair library number <#> (<#> = 1,2,3,4,5)
-*--mp<#>-2* <filename>::
-   file with reverse reads for mate-pair library number <#> (<#> = 1,2,3,4,5)
-*--mp<#>-s* <filename>::
-   file with unpaired reads for mate-pair library number <#> (<#> = 1,2,3,4,5)
-*--mp<#>-<or>*::
-   orientation of reads for mate-pair library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
-*--hqmp<#>-12* <filename>::
-  file with interlaced reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5)
-*--hqmp<#>-1* <filename>::
-   file with forward reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5)
-*--hqmp<#>-2* <filename>::
-   file with reverse reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5)
-*--hqmp<#>-s* <filename>::
-   file with unpaired reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5)
-*--hqmp<#>-<or>*::
-   orientation of reads for high-quality mate-pair library number <#> (<#> = 1,2,3,4,5; <or> = fr, rf, ff)
-*--nxmate<#>-1* <filename>::
-  file with forward reads for Lucigen NxMate library number <#> (<#> = 1,2,3,4,5)
-*--nxmate<#>-2* <filename>::
-  file with reverse reads for Lucigen NxMate library number <#> (<#> = 1,2,3,4,5)
-*--sanger* <filename>::
-  file with Sanger reads
-*--pacbio* <filename>::
-  file with PacBio reads
-*--nanopore* <filename>::
-   file with Nanopore reads
-*--trusted-contigs* <filename>::
-  file with trusted contigs
-*--untrusted-contigs* <filename>::
-   file with untrusted contigs
-
-### Input haplocontigs
-
-*--hap* <filename>::
-    file with haplocontigs
-
-### Pipeline options
-
-*--only-assembler*::
-     runs only assembling (without read error correction)
-*--disable-gzip-output*::
-    forces error correction not to compress the corrected reads
-*--disable-rr*::
-      disables repeat resolution stage of assembling
-
-### dipSPAdes options
-
-*--expect-gaps*::
-   indicates that significant number of gaps in coverage is expected
-*--expect-rearrangements*::
-   indicates that significant number of rearrangements between haplomes of diploid genome is expected
-*--hap-assembly*::
-   enables haplotype assembly phase
-
-### Advanced options
-
-*--dataset* <filename>::
-   file with dataset description in YAML format
-*-t*/*--threads* <int>::
-    number of threads [default: 16]
-*-m*/*--memory* <int>::
-    RAM limit for SPAdes in Gb (terminates if exceeded) [default: 250]
-*--tmp-dir* <dirname>::
-    directory for temporary files [default: <output_dir>/tmp]
-*-k* <int,int,...>::
-    comma-separated list of k-mer sizes (must be odd and less than 128) [default: 'auto']
-*--cov-cutoff* <float>::
-    coverage cutoff value (a positive float number, or 'auto', or 'off') [default: 'off']
-*--phred-offset* <33 or 64>::
-    PHRED quality offset in the input reads (33 or 64) [default: auto-detect]

debian/patches/0003_accept-system-bwa.patch

@@ -15,7 +15,7 @@ Description: Enable using Debian packaged bwa instead of bwa-spades
 
 --- a/src/spades_pipeline/support.py
 +++ b/src/spades_pipeline/support.py
-@@ -63,6 +63,22 @@ def warning(warn_str, log=None, prefix="
+@@ -61,6 +61,22 @@ def warning(warn_str, log=None, prefix="
          sys.stdout.write("\n\n" + prefix + " " + warn_str + "\n\n\n")
          sys.stdout.flush()
  
@@ -38,8 +38,8 @@ Description: Enable using Debian packaged bwa instead of bwa-spades
  
  def check_python_version():
      def __next_version(version):
-@@ -101,8 +117,14 @@ def check_binaries(binary_dir, log):
-     for binary in ["spades-hammer", "spades-ionhammer", "spades-core", "spades-bwa", "spades-dipspades-core"]:
+@@ -99,8 +115,14 @@ def check_binaries(binary_dir, log):
+     for binary in ["spades-hammer", "spades-ionhammer", "spades-core", "spades-bwa"]:
          binary_path = os.path.join(binary_dir, binary)
          if not os.path.isfile(binary_path):
 -            error("SPAdes binaries not found: " + binary_path + "\n" + get_spades_binaries_info_message(), log)
@@ -53,7 +53,7 @@ Description: Enable using Debian packaged bwa instead of bwa-spades
 +            else:
 +                error("SPAdes binaries not found: " + binary_path + "\n" + get_spades_binaries_info_message(), log)
  
- def check_file_existence(input_filename, message="", log=None, dipspades=False):
+ def check_file_existence(input_filename, message="", log=None):
      filename = abspath(expanduser(input_filename))
 --- a/spades.py
 +++ b/spades.py
@@ -80,7 +80,7 @@ Description: Enable using Debian packaged bwa instead of bwa-spades
  
  def fill_cfg(options_to_parse, log, secondary_filling=False):
      skip_output_dir = secondary_filling
-@@ -516,7 +532,11 @@ def fill_cfg(options_to_parse, log, seco
+@@ -513,7 +529,11 @@ def fill_cfg(options_to_parse, log, seco
      if (not options_storage.only_error_correction) and options_storage.mismatch_corrector:
          cfg["mismatch_corrector"] = empty_config()
          cfg["mismatch_corrector"].__dict__["skip-masked"] = None

debian/patches/0101_cmake_ignore_removed_python-yaml.patch

@@ -4,9 +4,9 @@ Description: Since we are using Debian packaged python-yaml
  (see 0001_use_debian_packaged_python-yaml.patch) the dir needs to be
  excluded
 
---- spades.orig/ext/src/CMakeLists.txt
-+++ spades/ext/src/CMakeLists.txt
-@@ -4,8 +4,6 @@
+--- a/ext/src/CMakeLists.txt
++++ b/ext/src/CMakeLists.txt
+@@ -4,8 +4,6 @@ add_subdirectory(jemalloc)
  add_subdirectory(nlopt)
  add_subdirectory(python_libs/joblib2)
  add_subdirectory(python_libs/joblib3)

debian/patches/0111_use_full_config_dirs.patch

@@ -4,7 +4,7 @@ Description: use full config include path
 Author: Sascha Steinbiss <satta@debian.org>
 --- a/src/spades_pipeline/spades_logic.py
 +++ b/src/spades_pipeline/spades_logic.py
-@@ -212,6 +212,20 @@ def run_iteration(configs_dir, execution
+@@ -211,6 +211,20 @@ def run_iteration(configs_dir, execution
  
      add_configs(command, dst_configs)
  
@@ -25,7 +25,7 @@ Author: Sascha Steinbiss <satta@debian.org>
      #print("Calling: " + " ".join(command))
      support.sys_call(command, log)
  
-@@ -259,6 +273,19 @@ def run_scaffold_correction(configs_dir,
+@@ -258,6 +272,19 @@ def run_scaffold_correction(configs_dir,
      command = [os.path.join(execution_home, "spades-truseq-scfcorrection"), cfg_file_name]
      add_configs(command, dst_configs)
      log.info(str(command))

debian/patches/series

@@ -7,7 +7,6 @@
 #adapt_to_debian_pathes.patch
 # use-debian-packaged-samtools.patch
 # bamtools-cmake.patch
-# use-debian-packaged-bamtools.patch   ## <<-- does not work - see patch description
 # use-debian-packaged-yaml-cpp.patch   ## <<-- does not work - see patch description
 0110_build_single_thread.patch
 0114_use_debian_provided_libs.patch

debian/patches/spelling

 From: Michael R. Crusoe <michael.crusoe@gmail.com>
 Subject: Spelling fixes
---- spades.orig/manual.html
-+++ spades/manual.html
-@@ -750,7 +750,7 @@
+--- a/manual.html
++++ b/manual.html
+@@ -753,7 +753,7 @@ For each file you should provide its ful
  Make sure that files with right reads are given in the same order as corresponding files with left reads.
  
  <p>
@@ -11,7 +11,7 @@ Subject: Spelling fixes
  <pre class="code">
  <code>
      lib_pe1_left_1.fastq
-@@ -979,7 +979,7 @@
+@@ -982,7 +982,7 @@ and PacBio CCS and CLR reads:
  </pre>
  
  <p>
@@ -20,7 +20,7 @@ Subject: Spelling fixes
  
  <pre class="code">
  <code>
-@@ -1128,7 +1128,7 @@
+@@ -1131,7 +1131,7 @@ Then, <code>contigs.paths</code> will co
  </pre>
  
  <p>
@@ -28,10 +28,10 @@ Subject: Spelling fixes
 +Since the current version of Bandage does not accept paths with gaps, paths corresponding contigs/scaffolds jumping over a gap in the assembly graph are split by semicolon at the gap positions. For example, the following record
  <pre>
      <code>
-     NODE_3_length_237403_cov_243.207_ID_45
---- spades.orig/src/common/assembly_graph/stats/picture_dump.hpp
-+++ spades/src/common/assembly_graph/stats/picture_dump.hpp
-@@ -123,7 +123,7 @@
+     NODE_3_length_237403_cov_243.207
+--- a/src/common/assembly_graph/stats/picture_dump.hpp
++++ b/src/common/assembly_graph/stats/picture_dump.hpp
+@@ -123,7 +123,7 @@ class GenomeMappingStat: public Abstract
          INFO("Genome mapping results:");
          INFO("Covered k+1-mers:" << covered_kp1mers << " of " << (genome_.size() - k_) << " which is "
               << (100.0 * (double) covered_kp1mers / (double) (genome_.size() - k_)) << "%");
@@ -40,74 +40,9 @@ Subject: Spelling fixes
          INFO("Continuity failtures " << fail);
      }
  };
---- spades.orig/src/projects/dipspades/kmer_gluing/equal_sequence_gluer.hpp
-+++ spades/src/projects/dipspades/kmer_gluing/equal_sequence_gluer.hpp
-@@ -74,9 +74,9 @@
-                 pos2 = graph_.length(edge1) - tmp - 1;
-             }
-             INFO(pos1 << " " << pos2 << " " << graph_.length(edge1))
--            TRACE("Edge1 " << graph_.int_id(edge1) << " will be splitted");
-+            TRACE("Edge1 " << graph_.int_id(edge1) << " will be split");
-             pair<EdgeId, EdgeId> split_edges = graph_.SplitEdge(edge1, pos1 + 1);
--            TRACE("Splitted pair was created");
-+            TRACE("Split pair was created");
-             TRACE("New edge1: " << graph_.int_id(split_edges.first) << ", length: " << graph_.length(split_edges.first));
-             TRACE("New edge2: " << graph_.int_id(split_edges.second) << ", length: " << graph_.length(split_edges.second));
-             edge1 = split_edges.first;
---- spades.orig/src/projects/dipspades/polymorphic_bulge_remover/bulge_gluer.hpp
-+++ spades/src/projects/dipspades/polymorphic_bulge_remover/bulge_gluer.hpp
-@@ -74,7 +74,7 @@
-         auto splitted_bulge = splitter_.SplitBulge(directed_bulge, glue_def_res);
- 
-         if(IsSplittedBulgeCorrect(splitted_bulge)){
--            TRACE("Splitted bulge correct");
-+            TRACE("Split bulge correct");
-             GlueSplittedBulge(splitted_bulge);
-             return true;
-         }
---- spades.orig/src/projects/dipspades/polymorphic_bulge_remover/bulge_splitter.hpp
-+++ spades/src/projects/dipspades/polymorphic_bulge_remover/bulge_splitter.hpp
-@@ -260,7 +260,7 @@
-         SplitOppositeEdge(split_res, split_paths.second, split_partlens.second);
- 
-         // update non splitted path
--        TRACE("Update non splitted path");
-+        TRACE("Update non split path");
-         if(num_splits.second != 0){
-             size_t edge_ind = vertices_to_split_[indexes.first].edge_ind_ + 1;
-             split_paths.first.push_back(default_paths.first[edge_ind]);
-@@ -298,7 +298,7 @@
- 
-         set<size_t> processed_indices;
-         while(num_done_splits < num_splits_.first + num_splits_.second){
--            TRACE("Splitted index - " << split_index << " , owner - " <<
-+            TRACE("Split index - " << split_index << " , owner - " <<
-                     vertices_to_split_[split_index].owner_path_);
- 
-             size_t opposite_index = IndexFirstOppositeEdge(split_index, processed_indices);
-@@ -418,8 +418,8 @@
-         if(!PerformSplitting(range1, range2))
-             return SplitResult(graph_);
- 
--        TRACE("Splitted spath1 - " << SimplePathWithVerticesToString(graph_, split_paths_.first));
--        TRACE("Splitted spath2 - " << SimplePathWithVerticesToString(graph_, split_paths_.second));
-+        TRACE("Split spath1 - " << SimplePathWithVerticesToString(graph_, split_paths_.first));
-+        TRACE("Split spath2 - " << SimplePathWithVerticesToString(graph_, split_paths_.second));
-         return SplitResult(graph_, split_paths_.first, split_paths_.second);
-     }
- 
-@@ -445,7 +445,7 @@
-             auto split_res = spaths_splitter.SplitSubpaths(
-                     subpath_range(0, bulge->path1().size() - 1),
-                     subpath_range(0, bulge->path2().size() - 1));
--            TRACE("bulge was splitted");
-+            TRACE("bulge was split");
-             TRACE("1st new bulge side - " << SimplePathWithVerticesToString(graph_, split_res.path1()));
-             TRACE("2nd new bulge side - " << SimplePathWithVerticesToString(graph_, split_res.path2()));
-             return shared_ptr<BaseBulge>(new Bulge(graph_, graph_.k(), split_res.path1(), split_res.path2()));
---- spades.orig/src/common/modules/alignment/pacbio/pac_index.hpp
-+++ spades/src/common/modules/alignment/pacbio/pac_index.hpp
-@@ -376,7 +376,7 @@
+--- a/src/common/modules/alignment/pacbio/pac_index.hpp
++++ b/src/common/modules/alignment/pacbio/pac_index.hpp
+@@ -376,7 +376,7 @@ public:
              auto next_iter = iter + 1;
              if (next_iter == cur_cluster.end() || !IsConsistent(**iter, **next_iter)) {
                  if (next_iter != cur_cluster.end()) {
@@ -116,9 +51,9 @@ Subject: Spelling fixes
                      DEBUG("on "<< (*iter)->str(g_));
                      DEBUG("and " << (*next_iter)->str(g_));
                  }
---- spades.orig/src/projects/hammer/hamcluster.cpp
-+++ spades/src/projects/hammer/hamcluster.cpp
-@@ -173,7 +173,7 @@
+--- a/src/projects/hammer/hamcluster.cpp
++++ b/src/projects/hammer/hamcluster.cpp
+@@ -173,7 +173,7 @@ void KMerHamClusterer::cluster(const std
  
    size_t big_blocks2 = 0;
    {