[med-svn] [Git][med-team/spades][master] 3 commits: Remove listed license files (ext/src/hmmer/libdivsufsort/COPYING) from copyright.
Andreas Tille (@tille)
gitlab at salsa.debian.org
Sun Feb 16 10:38:48 GMT 2025
Andreas Tille pushed to branch master at Debian Med / spades
Commits:
1aa75580 by Andreas Tille at 2025-02-15T16:51:15+00:00
Remove listed license files (ext/src/hmmer/libdivsufsort/COPYING) from copyright.
Changes-By: lintian-brush
Fixes: lintian: license-file-listed-in-debian-copyright
See-also: https://lintian.debian.org/tags/license-file-listed-in-debian-copyright.html
- - - - -
a2c956c6 by Andreas Tille at 2025-02-16T11:28:34+01:00
Seems unit test needs to run in same dir as config files. Move these to examples and enable users running it locally
- - - - -
dafceccd by Andreas Tille at 2025-02-16T11:36:22+01:00
Upload to unstable
- - - - -
29 changed files:
- + debian/README.test
- debian/changelog
- + debian/configs/README
- + debian/configs/careful_mda_mode.info
- + debian/configs/careful_mode.info
- + debian/configs/config.info
- + debian/configs/construction.info
- + debian/configs/detail_info_printer.info
- + debian/configs/distance_estimation.info
- + debian/configs/hmm_mode.info
- + debian/configs/isolate_mode.info
- + debian/configs/large_genome_mode.info
- + debian/configs/mda_mode.info
- + debian/configs/meta_mode.info
- + debian/configs/metaplasmid_mode.info
- + debian/configs/metaviral_mode.info
- + debian/configs/pe_params.info
- + debian/configs/plasmid_mode.info
- + debian/configs/rna_mode.info
- + debian/configs/rnaviral_mode.info
- + debian/configs/sewage_mode.info
- + debian/configs/simplification.info
- + debian/configs/toy.info
- debian/copyright
- debian/docs
- + debian/examples
- debian/tests/control
- + debian/tests/run-unit-test
- − debian/tests/run-upstreams-tests
Changes:
=====================================
debian/README.test
=====================================
@@ -0,0 +1,8 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+ sh run-unit-test
+
+in order to confirm its integrity.
=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+spades (4.0.0+dfsg1-2) unstable; urgency=low
+
+ Remove listed license files (ext/src/hmmer/libdivsufsort/COPYING) from copyright.
+
+ -- Andreas Tille <tille at debian.org> Sun, 16 Feb 2025 11:28:59 +0100
+
spades (4.0.0+dfsg1-1) experimental; urgency=medium
* Team upload
=====================================
debian/configs/README
=====================================
@@ -0,0 +1,6 @@
+These configs were created using
+
+ spades --test
+
+and copied here from the resulting spades_test/K21/configs
+
=====================================
debian/configs/careful_mda_mode.info
=====================================
@@ -0,0 +1,40 @@
+simp
+{
+ ; bulge remover:
+ br
+ {
+ enabled true
+ max_relative_coverage 1.1 ; bulge_cov < this * not_bulge_cov
+ }
+
+ ; complex bulge remover
+ cbr
+ {
+ enabled false
+ }
+
+ final_tc
+ {
+ condition ""
+ }
+
+ ; bulge remover:
+ final_br
+ {
+ enabled false
+ }
+
+ init_clean
+ {
+ early_it_only true
+
+ activation_cov -1.
+ ier
+ {
+ enabled false
+ }
+
+ tip_condition ""
+ ec_condition ""
+ }
+}
=====================================
debian/configs/careful_mode.info
=====================================
@@ -0,0 +1,42 @@
+simp
+{
+ ; bulge remover:
+ br
+ {
+ enabled true
+ max_relative_coverage 0.5 ; bulge_cov < this * not_bulge_cov
+ ; parallel false
+ }
+
+ ; complex bulge remover
+ cbr
+ {
+ enabled false
+ }
+
+ ; bulge remover:
+ final_br
+ {
+ enabled false
+ }
+
+ ; relative coverage erroneous component remover:
+ rcc
+ {
+ enabled false
+ }
+
+ init_clean
+ {
+ early_it_only true
+
+ activation_cov -1.
+ ier
+ {
+ enabled false
+ }
+
+ tip_condition ""
+ ec_condition ""
+ }
+}
=====================================
debian/configs/config.info
=====================================
@@ -0,0 +1,216 @@
+; input options:
+
+#include "simplification.info"
+#include "construction.info"
+#include "distance_estimation.info"
+#include "detail_info_printer.info"
+#include "pe_params.info"
+
+K 21
+;FIXME introduce isolate mode
+mode base
+
+dataset /home/andreas/debian-maintain/salsa/med-team/spades/spades_test/dataset.info
+log_filename log.properties
+
+output_base /home/andreas/debian-maintain/salsa/med-team/spades/spades_test
+tmp_dir /home/andreas/debian-maintain/salsa/med-team/spades/spades_test/tmp/spades_czd68ryh
+
+main_iteration false
+; iterative mode switcher, activates additional contigs usage
+use_additional_contigs false
+additional_contigs tmp_contigs.fasta
+load_from /home/andreas/debian-maintain/salsa/med-team/spades/spades_test/K21/saves
+
+; Multithreading options
+temp_bin_reads_dir .bin_reads/
+max_threads 16
+max_memory 62
+buffer_size 512; in Megabytes
+
+entry_point read_conversion
+;entry_point construction
+;entry_point simplification
+;entry_point hybrid_aligning
+;entry_point late_pair_info_count
+;entry_point distance_estimation
+;entry_point repeat_resolving
+
+checkpoints none
+developer_mode false
+sewage false
+sewage_matrix /usr/share/spades/sewage/usher_barcodes.csv
+
+scaffold_correction_mode false
+
+; enabled (1) or disabled (0) repeat resolution (former "paired_mode")
+rr_enable false
+; 0 for graph N50
+min_edge_length_for_is_count 0
+
+; Whether GFA v1.2 (jump links) or GFA v1.1 (scaffold segments) graphs is written
+gfa11 false
+
+;preserve raw paired index after distance estimation
+preserve_raw_paired_index false
+
+; two-step pipeline
+two_step_rr false
+; enables/disables usage of intermediate contigs in two-step pipeline
+use_intermediate_contigs false
+
+;use single reads for rr (all | only_single_libs | none )
+single_reads_rr only_single_libs
+
+; The following parameters are used ONLY if developer_mode is true
+
+; whether to output dot-files with pictures of graphs - ONLY in developer mode
+output_pictures true
+
+; whether to output resulting contigs after intermediate stages - ONLY in developer mode
+output_nonfinal_contigs true
+
+; whether to compute number of paths statistics - ONLY in developer mode
+compute_paths_number false
+
+; End of developer_mode parameters
+
+;if true simple mismatches are corrected
+correct_mismatches false
+
+; set it true to get statistics, such as false positive/negative, perfect match, etc.
+paired_info_statistics false
+
+; set it true to get statistics for pair information (over gaps), such as false positive/negative, perfect match, etc.
+paired_info_scaffolder false
+
+;the only option left from repeat resolving
+max_repeat_length 8000
+
+; repeat resolving mode (none path_extend)
+resolving_mode path_extend
+
+use_scaffolder true
+
+avoid_rc_connections true
+
+calculate_coverage_for_each_lib false
+strand_specificity {
+ ss_enabled false
+ antisense false
+}
+
+contig_output {
+ contigs_name final_contigs
+ scaffolds_name scaffolds
+ ; none --- do not output broken scaffolds | break_gaps --- break only by N steches | break_all --- break all with overlap < k
+ output_broken_scaffolds break_gaps
+}
+
+;position handling
+
+pos
+{
+ max_mapping_gap 0 ; in terms of K+1 mers value will be K + max_mapping_gap
+ max_gap_diff 0
+ contigs_for_threading ./data/debruijn/contigs.fasta
+ contigs_to_analyze ./data/debruijn/contigs.fasta
+ late_threading true
+ careful_labeling true
+
+}
+
+gap_closer_enable false
+
+gap_closer
+{
+ minimal_intersection 10
+
+ ;before_raw_simplify and before_simplify are mutually exclusive
+ before_raw_simplify true
+ before_simplify false
+ after_simplify true
+ weight_threshold 2.0
+ max_dist_to_tip 5000
+}
+
+kmer_coverage_model {
+ probability_threshold 0.05
+ strong_probability_threshold 0.999
+ use_coverage_threshold false
+ coverage_threshold 10.0
+}
+
+; low covered edges remover
+lcer
+{
+ lcer_enabled false
+ lcer_coverage_threshold 0.0
+}
+
+pacbio_processor ;commented frozen constants default assinged in hpp
+{
+ internal_length_cutoff 200
+;align and traverse.
+; compression_cutoff 0.6
+; path_limit_stretching 1.3
+; path_limit_pressing 0.7
+ max_path_in_dijkstra 15000
+ max_vertex_in_dijkstra 2000
+ rna_filtering false
+
+;gap_closer
+ long_seq_limit 400
+ enable_gap_closing true
+ pacbio_min_gap_quantity 2
+ contigs_min_gap_quantity 1
+ max_contigs_gap_length 10000
+;spoa
+; match 5
+; mismatch -4
+; gap_open -8
+; gap_extend -6
+; gap_open_second -10
+; gap_extend_second -4
+}
+
+;TODO move out!
+graph_read_corr
+{
+ enable false
+ output_dir corrected_contigs/
+ binary true
+}
+
+bwa_aligner
+{
+ debug false
+ min_contig_len 0
+}
+
+;flanking coverage range
+flanking_range 55
+series_analysis ""
+save_gp false
+
+ss_coverage_splitter {
+ enabled false
+ bin_size 50
+ min_edge_len 200
+ min_edge_coverage 5
+ min_flanking_coverage 2
+ coverage_margin 5
+}
+
+time_tracer {
+ time_tracer_enabled false
+ granularity 500
+}
+
+hybrid_aligner {
+ trusted_aligner {
+ long_read_threshold 1000
+ long_read_fuzzy_coverage 0.95
+ short_read_fuzzy_coverage 0.90
+ }
+}
=====================================
debian/configs/construction.info
=====================================
@@ -0,0 +1,26 @@
+; construction
+
+construction
+{
+ ; mode of construction: extension (construct hash map of kmers to extentions), old (construct set of k+1-mers)
+ mode extension
+
+ ; enable keeping in graph perfect cycles. This slows down condensing but some plasmids can be lost if this is turned off.
+ keep_perfect_loops true
+
+ ; size of buffer for each thread in MB, 0 for autodetection
+ read_buffer_size 0
+
+ ; read median coverage threshold
+ read_cov_threshold 0
+
+ early_tip_clipper
+ {
+ ; tip clipper can be enabled only in extension mode
+ enable true
+
+ ; optional parameter. By default tips of length rl-k are removed
+; length_bound 10
+ }
+}
+
=====================================
debian/configs/detail_info_printer.info
=====================================
@@ -0,0 +1,46 @@
+info_printers
+{
+ default
+ {
+ basic_stats false
+ lib_info false
+ save_all false
+ save_full_graph false
+ save_graph_pack false
+ extended_stats false
+ detailed_dot_write false
+ write_components false
+ components_for_genome_pos "" ; (k+1)-mers starting on this positions will be investigated
+ components_for_kmer ""
+ write_components_along_genome false
+ write_components_along_contigs false
+ write_error_loc false
+ write_full_graph false
+ write_full_nc_graph false
+ }
+
+ before_first_gap_closer
+ {
+ }
+
+ before_simplification
+ {
+ }
+
+ before_post_simplification
+ {
+ }
+
+ final_simplified
+ {
+ }
+
+ final_gap_closed
+ {
+ }
+
+ before_repeat_resolution
+ {
+ }
+
+}
=====================================
debian/configs/distance_estimation.info
=====================================
@@ -0,0 +1,42 @@
+; distance estimator:
+
+de
+{
+ linkage_distance_coeff 0.0
+ max_distance_coeff 2.0
+ max_distance_coeff_scaff 2000.0
+ clustered_filter_threshold 2.0
+ raw_filter_threshold 2
+ rounding_coeff 0.5 ; rounding : min(de_max_distance * rounding_coeff, rounding_thr)
+ rounding_threshold 0
+}
+
+ade
+{
+ ;data dividing
+ threshold 80 ;maximal distance between two points in cluster
+
+ ;local maximum seeking
+ range_coeff 0.2 ;data_length*range_coeff := width of the averaging window
+ delta_coeff 0.4 ;data_length*delta_coeff := maximal difference between possible distance and real peak on the graph
+
+ ;fft smoothing
+ percentage 0.01 ;percent of data for baseline subraction
+ cutoff 3 ;the number of the lowest freqs in fourier decomp being taken
+
+ ;other
+ min_peak_points 3 ;the minimal number of points in cluster to be considered
+ inv_density 5.0 ;maximal inverse density of points in cluster to be considered
+
+ ;hard_mode arguments
+ derivative_threshold 0.2 ;threshold for derivative in hard mode
+
+}
+
+; ambiguous pair info checker parameters
+amb_de {
+ enabled false
+ haplom_threshold 500
+ relative_length_threshold 0.8
+ relative_seq_threshold 0.5
+}
=====================================
debian/configs/hmm_mode.info
=====================================
@@ -0,0 +1,6 @@
+hmm_match {
+ set_of_hmms none
+ component_size_part 10
+ start_only_from_tips false
+ set_copynumber false
+}
=====================================
debian/configs/isolate_mode.info
=====================================
@@ -0,0 +1,4 @@
+mode isolate
+
+#include "careful_mode.info"
+
=====================================
debian/configs/large_genome_mode.info
=====================================
@@ -0,0 +1,11 @@
+;FIXME do we still need this mode?
+mode large_genome
+
+pe {
+
+debug_output false
+
+params {
+ scaffolding_mode old_pe_2015
+}
+}
=====================================
debian/configs/mda_mode.info
=====================================
@@ -0,0 +1,105 @@
+mode mda
+
+simp
+{
+ ; enable advanced ec removal algo
+ topology_simplif_enabled true
+
+ ; tip clipper:
+ tc
+ {
+ ; rctc: tip_cov < rctc * not_tip_cov
+ ; tc_lb: max_tip_length = max((min(k, read_length / 2) * tc_lb), read_length);
+ condition "{ tc_lb 3.5, cb 1000000, rctc 2.0 }"
+ }
+
+ ; erroneous connections remover:
+ ec
+ {
+ ; ec_lb: max_ec_length = k + ec_lb
+ ; icb: iterative coverage bound
+ ; condition "{ ec_lb 30, icb 20.0 }"
+ condition "{ ec_lb 30, icb auto }"
+ }
+
+ final_tc
+ {
+ condition "{ tc_lb 3.5, cb 100000, rctc 10000 }"
+ }
+
+ ; bulge remover:
+ final_br
+ {
+ enabled true
+ max_coverage 1000000.0
+ max_relative_coverage 100000. ; bulge_cov < this * not_bulge_cov
+ }
+
+ ; relative coverage erroneous component remover:
+ rcc
+ {
+ enabled true
+ coverage_gap 10.
+ max_length_coeff 2.0
+ max_length_with_tips_coeff 3.0
+ max_vertex_cnt 30
+ max_ec_length_coefficient 30
+ max_coverage_coeff 5.0
+ }
+
+ ; complex bulge remover
+ cbr
+ {
+ enabled true
+ }
+
+ ; hidden ec remover
+ her
+ {
+ enabled true
+ uniqueness_length 1500
+ unreliability_threshold 0.2
+ relative_threshold 5
+ }
+
+ init_clean
+ {
+ activation_cov -1.
+ ier
+ {
+ enabled false
+ }
+
+ tip_condition ""
+ ec_condition ""
+ }
+}
+
+de
+{
+ raw_filter_threshold 0
+ rounding_threshold 0
+}
+
+
+pe {
+params {
+ normalize_weight true
+
+ scaffolding_mode old
+
+ ; extension selection
+ extension_options
+ {
+ single_threshold 0.3
+ weight_threshold 0.6
+ max_repeat_length 8000
+ }
+}
+
+long_reads {
+ pacbio_reads {
+ unique_edge_priority 10.0
+ }
+}
+}
=====================================
debian/configs/meta_mode.info
=====================================
@@ -0,0 +1,227 @@
+mode meta
+
+; two-step pipeline
+two_step_rr true
+min_edge_length_for_is_count 900
+
+; enables/disables usage of intermediate contigs in two-step pipeline
+use_intermediate_contigs true
+
+;flanking coverage range
+flanking_range 30
+
+simp
+{
+ cycle_iter_count 3
+
+ ; enable advanced ec removal algo
+ topology_simplif_enabled false
+
+ ; erroneous connections remover:
+ ec
+ {
+ ; ec_lb: max_ec_length = k + ec_lb
+ ; icb: iterative coverage bound
+ ; condition "{ ec_lb 30, icb 20.0 }"
+ condition "{ ec_lb 30, icb 2.5 }"
+ }
+
+ ; tip clipper:
+ tc
+ {
+ ; rctc: tip_cov < rctc * not_tip_cov
+ ; tc_lb: max_tip_length = max((min(k, read_length / 2) * tc_lb), read_length);
+ condition "{ rl 0.2 } { rlmk 2., rctc 2.0 }"
+ }
+
+ ; relative coverage erroneous component remover:
+ rcc
+ {
+ enabled true
+ coverage_gap 5.
+ max_length_coeff 3.0
+ max_length_with_tips_coeff 5.0
+ max_vertex_cnt 100
+ max_ec_length_coefficient 300
+ max_coverage_coeff -1.0
+ }
+
+ ; complex tip clipper
+ complex_tc
+ {
+ enabled true
+ }
+
+ ; relative edge disconnector:
+ red
+ {
+ enabled true
+ diff_mult 10.
+ unconditional_diff_mult 50.
+ }
+
+ ; bulge remover:
+ br
+ {
+ enabled true
+ max_coverage 1000000.0
+ max_relative_coverage 5. ; bulge_cov < this * not_bulge_cov
+ max_delta 10
+ max_relative_delta 0.1
+ dijkstra_vertex_limit 3000
+ parallel true
+ }
+
+ ; final tip clipper:
+ final_tc
+ {
+ condition "{ lb 500, rctc 0.4 } { lb 850, rctc 0.2 }"
+ }
+
+ ; final bulge remover:
+ final_br
+ {
+ enabled true
+ main_iteration_only true
+ max_bulge_length_coefficient 30. ; max_bulge_length = max_bulge_length_coefficient * k
+ max_coverage 1000000.0
+ max_relative_coverage 0.5 ; bulge_cov < this * not_bulge_cov
+ max_delta 45
+ max_relative_delta 0.1
+ min_identity 0.7
+ }
+
+ ; suspecies bulge remover:
+ subspecies_br
+ {
+ enabled false
+ }
+
+ ; complex bulge remover
+ cbr
+ {
+ enabled true
+ }
+
+ ; hidden ec remover
+ her
+ {
+ ; TODO NB config used in special meta mode version (always enabled)
+ enabled false
+ uniqueness_length 1500
+ unreliability_threshold -1.
+ relative_threshold 3.
+ }
+
+ init_clean
+ {
+ activation_cov -1.
+ early_it_only false
+ ier
+ {
+ enabled true
+ }
+ ;Disable if it does not help the br performance much!
+ tip_condition "{ tc_lb 3.5, cb 2.1 }"
+ ;ec_condition is here only to speed-up future br on early iterations
+ ec_condition "{ ec_lb 10, cb 1.5 }"
+ disconnect_flank_cov -1.
+ }
+
+}
+
+;TODO rename
+preliminary_simp
+{
+ init_clean
+ {
+ tip_condition "loop 2 { rlmk 1., cb 1.2, mmm 2 } { rlmk 1., cb 1.2, mmm 0.05 } { rl 0.2, cb 1.2 }"
+ ec_condition "{ ec_lb 0, cb 0.9 }"
+ disconnect_flank_cov 0.8
+ }
+
+ ; bulge remover:
+ br
+ {
+ enabled true
+ max_coverage 1000000.0
+ max_relative_coverage 0.5 ; bulge_cov < this * not_bulge_cov
+ max_delta 10
+ max_relative_delta 0.1
+ }
+
+ ; Currently will not work even if enabled. Left for experiments.
+ ; relative edge disconnector
+ red
+ {
+ enabled false
+ diff_mult 10.
+ unconditional_diff_mult 100.
+ }
+}
+
+; undo single cell config changes, enforce filtering
+de
+{
+ raw_filter_threshold 1
+ rounding_coeff 0.5 ; rounding : min(de_max_distance * rounding_coeff, rounding_thr)
+ rounding_threshold 0
+}
+
+;NB decsends from sc_pe
+pe {
+
+long_reads {
+ pacbio_reads {
+ filtering 1.9
+ weight_priority 20.0
+ unique_edge_priority 10.0
+ min_significant_overlap 1000
+ }
+}
+
+params {
+ overlap_removal {
+ enabled true
+ cut_all true
+ }
+
+ scaffolding_mode old_pe_2015
+
+ normalize_weight true
+
+ ; extension selection
+ extension_options
+ {
+ single_threshold 0.3
+ weight_threshold 0.6
+ priority_coeff 1.5
+ max_repeat_length 1000000
+ }
+
+ use_coordinated_coverage true
+
+ coordinated_coverage
+ {
+ min_path_len 10000
+ }
+
+}
+
+}
+
+prelim_pe {
+params {
+ scaffolding_mode old
+
+ overlap_removal {
+ enabled false
+ }
+
+ use_coordinated_coverage false
+ remove_overlaps false
+ scaffolding2015 {
+ min_unique_length 100000000
+ }
+}
+}
=====================================
debian/configs/metaplasmid_mode.info
=====================================
@@ -0,0 +1,3 @@
+mode metaextrachromosomal
+two_step_rr false
+
=====================================
debian/configs/metaviral_mode.info
=====================================
@@ -0,0 +1,40 @@
+mode metaextrachromosomal
+two_step_rr false
+
+simp
+{
+
+ ; suspecies bulge remover:
+ subspecies_br
+ {
+ enabled true
+ main_iteration_only true
+ max_bulge_length_coefficient 30. ; max_bulge_length = max_bulge_length_coefficient * k
+ max_coverage 1000000.0
+ max_relative_coverage 15 ; bulge_cov < this * not_bulge_cov
+ max_delta 45
+ max_relative_delta 0.2
+ min_identity 0.7
+ }
+
+}
+plasmid
+{
+;isolated
+ long_edge_length 1000
+ edge_length_for_median 10000
+ relative_coverage 0.3
+ small_component_size 10000
+ small_component_relative_coverage 1.5
+ min_component_length 10000
+ min_isolated_length 1000
+; reference_removal replace this with path to reference and uncomment for reference based filtration
+;meta
+ iterative_coverage_elimination true
+ additive_step 5
+ relative_step 1.3
+ max_length 1000000
+ output_linear true
+ min_circular_length 1000
+ min_linear_length 500
+}
=====================================
debian/configs/pe_params.info
=====================================
@@ -0,0 +1,179 @@
+pe {
+
+; output options
+
+debug_output false
+
+output {
+ write_overlaped_paths true
+ write_paths true
+}
+
+visualize {
+ print_overlaped_paths true
+ print_paths true
+}
+
+params {
+ multi_path_extend false
+ ; old | 2015 | combined | old_pe_2015
+ scaffolding_mode old_pe_2015
+
+ overlap_removal {
+ enabled true
+ end_start_only false
+ cut_all false
+ }
+
+ normalize_weight true
+
+ ; extension selection
+ extension_options
+ {
+ single_threshold 0.1
+ weight_threshold 0.5
+ priority_coeff 1.5
+ ;TODO remove from here
+ max_repeat_length 8000
+ }
+
+ mate_pair_options
+ {
+ single_threshold 30
+ weight_threshold 0.5
+ priority_coeff 1.5
+ ;TODO remove from here
+ max_repeat_length 8000
+ }
+
+ scaffolder {
+ enabled true
+ cutoff 2
+ hard_cutoff 0
+ rel_cov_cutoff 0.0
+ sum_threshold 3
+
+ cluster_info true
+ cl_threshold 0
+
+ fix_gaps true
+ use_la_gap_joiner true
+ ;next param should be 0.51 - 1.0 if use_old_score = true and 3.0 otherwise
+ min_gap_score 0.7
+
+ max_can_overlap 1.
+ short_overlap 6
+ artificial_gap 10
+
+ min_overlap_length 10
+ flank_multiplication_coefficient .5
+ flank_addition_coefficient 5
+
+ var_coeff 3.0
+ basic_overlap_coeff 2.0
+ }
+
+ path_cleaning_presets ""
+
+ use_coordinated_coverage false
+ coordinated_coverage
+ {
+ max_edge_length_repeat 300
+ delta 0.5
+ min_path_len 1000
+ }
+
+
+ simple_coverage_resolver {
+ enabled false
+ coverage_margin 2
+ min_upper_coverage 5
+ max_coverage_variation 5
+ }
+
+
+ scaffolding2015 {
+ ; (median * (1+variation) > unique > median * (1 - variation))
+ relative_weight_cutoff 2.0
+
+ unique_length_upper_bound 2000 ; max(unique_length_upper_bound, max_is(all libs))
+ unique_length_lower_bound 500 ; max(unique_length_lower_bound, unique_length_step)
+ unique_length_step 300
+
+ graph_connectivity_max_edges 200000
+ }
+
+ scaffold_graph {
+ construct false
+ output false
+ always_add 40 ; connection with read count >= always_add are always added to the graph
+ never_add 5 ; connection with read count < never_add are never added to the graph
+ relative_threshold 0.25 ; connection with read count >= max_read_count * relative_threshod are added to the graph if satisfy condition above, max_read_count is calculated amond all alternatives
+ use_graph_connectivity false
+ max_path_length 10000
+ }
+
+ genome_consistency_checker {
+ max_gap 1000
+ relative_max_gap 0.2
+ use_main_storage true ; if set to true, next two parameters are set to min_unique_length
+ unresolvable_jump 1000 ; length of unresolvable repeats
+ unique_length 500 ; spelling genome in the alphabet of edges longer than this
+ }
+
+ uniqueness_analyser {
+ enabled true
+ unique_coverage_variation 0.5
+
+ nonuniform_coverage_variation 50
+ uniformity_fraction_threshold 0.8
+ }
+
+ loop_traversal
+ {
+ min_edge_length 1000
+ max_component_size 10
+ max_path_length 1000
+ }
+}
+
+
+long_reads {
+ pacbio_reads {
+ filtering 2.5
+ weight_priority 1.2
+ unique_edge_priority 5.0
+ min_significant_overlap 0
+ }
+
+ single_reads {
+ filtering 1.25
+ weight_priority 5.0
+ unique_edge_priority 10000.0
+ min_significant_overlap 0
+ }
+
+ contigs {
+ filtering 0.0
+ weight_priority 1.5
+ unique_edge_priority 2.0
+ min_significant_overlap 0
+ }
+
+ meta_untrusted_contigs {
+ filtering 0.0
+ weight_priority 10000.0
+ unique_edge_priority 10000.0
+ min_significant_overlap 200
+ }
+
+ rna_long_reads {
+ filtering 0.1
+ weight_priority 1.1
+ unique_edge_priority 2.0
+ min_significant_overlap 0
+ }
+
+
+}
+}
=====================================
debian/configs/plasmid_mode.info
=====================================
@@ -0,0 +1,22 @@
+mode plasmid
+
+plasmid
+{
+;isolated
+ long_edge_length 1000
+ edge_length_for_median 10000
+ relative_coverage 0.3
+ small_component_size 10000
+ small_component_relative_coverage 1.5
+ min_component_length 10000
+ min_isolated_length 1000
+; reference_removal replace this with path to reference and uncomment for reference based filtration
+;meta
+ iterative_coverage_elimination true
+ additive_step 5
+ relative_step 1.3
+ max_length 1000000
+ output_linear false
+ min_circular_length 1000
+ min_linear_length 500
+}
=====================================
debian/configs/rna_mode.info
=====================================
@@ -0,0 +1,213 @@
+mode rna
+
+preserve_raw_paired_index true
+min_edge_length_for_is_count 500
+
+calculate_coverage_for_each_lib true
+strand_specificity {
+ ss_enabled false
+ antisense false
+}
+
+ss_coverage_splitter {
+ enabled true
+ bin_size 50
+ min_edge_len 200
+ min_edge_coverage 5
+ min_flanking_coverage 2
+ coverage_margin 5
+}
+
+pacbio_processor
+{
+ internal_length_cutoff 100
+;align and traverse.
+; compression_cutoff 0.6
+; path_limit_stretching 1.3
+; path_limit_pressing 0.7
+ max_path_in_dijkstra 5000
+ max_vertex_in_dijkstra 1000
+ rna_filtering true
+
+;gap_closer
+ long_seq_limit 100
+ enable_gap_closing false
+ enable_fl_gap_closing true
+ pacbio_min_gap_quantity 2
+ contigs_min_gap_quantity 1
+ max_contigs_gap_length 10000
+}
+
+contig_output {
+ scaffolds_name transcripts
+ ; none --- do not output broken scaffolds | break_gaps --- break only by N steches | break_all --- break all with overlap < k
+ output_broken_scaffolds none
+}
+
+simp
+{
+ ;all topology based erroneous connection removers are off
+ topology_simplif_enabled false
+
+ tc
+ {
+ ; rctc: tip_cov < rctc * not_tip_cov
+ ; tc_lb: max_tip_length = max((min(k, read_length / 2) * tc_lb), read_length);
+ condition "{ mmm 3 tc_lb 4, cb 100000, rctc 0.5 } { tc_lb 2, cb 1, rctc 10000 }"
+ }
+
+ dead_end
+ {
+ enabled true
+ condition "{ tc_lb 3.5, cb 2 }"
+ }
+
+ ; bulge remover:
+ br
+ {
+ enabled true
+ max_additive_length_coefficient 100
+ max_coverage 1000000.0
+ max_relative_coverage 100000.0 ; bulge_cov < this * not_bulge_cov
+ }
+
+ ; erroneous connections remover:
+ ec
+ {
+ ; ec_lb: max_ec_length = k + ec_lb
+ ; icb: iterative coverage bound
+ ; to_ec_lb: max_ec_length = 2*tip_length(to_ec_lb) - 1
+ ; nbr: use not bulge erroneous connections remover
+ ; condition "{ ec_lb 9, icb 40.0, nbr }"
+ condition "{ ec_lb 30, icb 200, rcec_cb 1.0 }"
+ }
+
+ ; relative coverage erroneous connections remover:
+ rcec
+ {
+ rcec_lb 30
+ rcec_cb 1.0
+ enabled true
+ }
+
+ rcc
+ {
+ enabled true
+ coverage_gap 20.
+ }
+
+ ; hidden ec remover
+ her
+ {
+ ; TODO NB config also used in special rna mode version (always enabled)
+ enabled false
+ uniqueness_length 1500
+ unreliability_threshold 0.2
+ relative_threshold 5
+ }
+
+ ier
+ {
+ enabled true
+ use_rl_for_max_length true ; max_length will be taken max with read_length
+ use_rl_for_max_length_any_cov false ; use_rl_for_max_length_any_cov will be taken max with read_length
+ max_length 80
+ max_coverage 2
+ max_length_any_cov 0
+ rl_threshold_increase 2 ; add this value to read length if used, i.e. flags above are set
+ }
+
+}
+
+; disable filtering in rna mode
+de
+{
+ raw_filter_threshold 0
+}
+
+pe {
+debug_output true
+
+params {
+ multi_path_extend true
+
+ scaffolding_mode old
+
+ overlap_removal {
+ enabled false
+ end_start_only true
+ cut_all true
+ }
+
+ extension_options
+ {
+ single_threshold 0.05
+ }
+
+ scaffolder {
+ cutoff 1
+ hard_cutoff 5
+ rel_cov_cutoff 0.1
+ cluster_info false
+ min_overlap_for_rna_scaffolding 8
+ }
+
+ path_cleaning_presets "default soft hard"
+ ; All length cutoffs presented in nucleotides
+ ; So edges less than or equal to (relative cutoff * RL - K) or (absolute cutoff - K) will be deleted
+ path_cleaning
+ {
+ enabled true
+ min_length 110
+ isolated_min_length 130
+ isolated_min_cov 4
+ min_length_for_low_covered 140
+ rel_cutoff 1.3
+ rel_isolated_cutoff 1.5
+ rel_low_covered_cutoff 1.6
+ min_coverage 2
+ }
+
+ ; All length cutoffs presented in nucleotides
+ hard_path_cleaning
+ {
+ enabled true
+ min_length 130
+ isolated_min_length 180
+ isolated_min_cov 8
+ min_length_for_low_covered 180
+ rel_cutoff 1.5
+ rel_isolated_cutoff 2.0
+ rel_low_covered_cutoff 2.0
+ min_coverage 3
+ }
+
+ ; All length cutoffs presented in nucleotides
+ soft_path_cleaning
+ {
+ enabled true
+ min_length 85
+ isolated_min_length 100
+ isolated_min_cov 2
+ min_length_for_low_covered 130
+ rel_cutoff 1.05
+ rel_isolated_cutoff 1.2
+ rel_low_covered_cutoff 1.5
+ min_coverage 1
+ }
+
+ use_coordinated_coverage false
+ coordinated_coverage {
+ max_edge_length_repeat 1000
+ delta 0.5
+ min_path_len 300
+ }
+
+ simple_coverage_resolver {
+ enabled true
+ coverage_margin 2
+ min_upper_coverage 2
+ max_coverage_variation 10
+ }
+}
+}
=====================================
debian/configs/rnaviral_mode.info
=====================================
@@ -0,0 +1,32 @@
+mode rnaviral
+two_step_rr false
+
+simp
+{
+
+ ; suspecies bulge remover:
+ subspecies_br
+ {
+ enabled true
+ main_iteration_only true
+ max_bulge_length_coefficient 30. ; max_bulge_length = max_bulge_length_coefficient * k
+ max_coverage 1000000.0
+ max_relative_coverage 15 ; bulge_cov < this * not_bulge_cov
+ max_delta 45
+ max_relative_delta 0.2
+ min_identity 0.9
+ }
+
+ red
+ {
+ enabled true
+ diff_mult 10.
+ unconditional_diff_mult 50.
+ edge_sum 0
+ }
+
+ final_br
+ {
+ enabled false
+ }
+}
=====================================
debian/configs/sewage_mode.info
=====================================
@@ -0,0 +1,61 @@
+simp {
+ ; bulge remover:
+ br
+ {
+ enabled true
+ max_coverage 10.0
+ max_relative_coverage 0.05 ; bulge_cov < this * not_bulge_cov
+ max_delta 10
+ max_relative_delta 0.1
+ dijkstra_vertex_limit 3000
+ parallel true
+ }
+ ; final bulge remover:
+ final_br
+ {
+ enabled false
+ }
+ ; complex bulge remover
+ cbr
+ {
+ enabled false
+ }
+ ; relative coverage erroneous component remover:
+ rcc
+ {
+ enabled true
+ coverage_gap 15.
+ max_length_coeff 3.0
+ max_length_with_tips_coeff 5.0
+ max_vertex_cnt 100
+ max_ec_length_coefficient 300
+ max_coverage_coeff -1.0
+ }
+
+ ; tip clipper:
+ tc
+ {
+ ; rctc: tip_cov < rctc * not_tip_cov
+ ; tc_lb: max_tip_length = max((min(k, read_length / 2) * tc_lb), read_length);
+ condition "{ rl 0.2, cb 10.0 } { rlmk 1.1, rctc 2.0, cb 10.0 }"
+ }
+
+ final_tc
+ {
+ condition ""
+ }
+}
+
+preliminary_simp
+{
+ ; bulge remover:
+ br
+ {
+ enabled true
+ max_coverage 500.0
+ max_relative_coverage 0.5 ; bulge_cov < this * not_bulge_cov
+ max_delta 10
+ max_relative_delta 0.1
+ }
+
+}
=====================================
debian/configs/simplification.info
=====================================
@@ -0,0 +1,244 @@
+; simplification
+
+simp
+{
+ ; ==== RAW SIMPLIFICATION ====
+ init_clean
+ {
+ self_conj_condition "{ ec_lb 100, cb 1.0 }"
+ early_it_only false
+ ; will be enabled only if average coverage >= activate_cov
+ ; if value < 0 check not performed
+ activation_cov 10.
+
+ ; isolated edges remover
+ ier
+ {
+ enabled true
+ use_rl_for_max_length false ; max_length will be taken max with read_length
+ use_rl_for_max_length_any_cov true ; use_rl_for_max_length_any_cov will be taken max with read_length
+ max_length 0 ; will be taken max with read_length if option above is set
+ max_coverage 0
+ max_length_any_cov 0 ; will be taken max with read_length if option above is set
+ rl_threshold_increase 0 ; add this value to read length if used, i.e. flags above are set
+ }
+
+ tip_condition "{ tc_lb 3.5, cb auto }"
+ ec_condition "{ ec_lb 10, cb 2.0 }"
+
+ ; edges with flank cov around alternative less than value will be disconnected
+ ; negative value to disable
+ disconnect_flank_cov -1.0
+ }
+
+ ; ==== SIMPLIFICATION CYCLE ====
+
+ ; number of iterations in basic simplification cycle
+ cycle_iter_count 10
+
+ ; tip clipper:
+ tc
+ {
+ ; rctc: tip_cov < rctc * not_tip_cov
+ ; tc_lb: max_tip_length = max((min(k, read_length / 2) * tc_lb), read_length);
+ ; todo think about params one more time
+ condition "{ tc_lb 3.5, cb 1000000, rctc 2.0 } { tc_lb 10., cb auto }"
+ }
+
+ ; bulge remover:
+ br
+ {
+ enabled true
+ main_iteration_only false
+ max_bulge_length_coefficient 3. ; max_bulge_length = max_bulge_length_coefficient * k
+ max_additive_length_coefficient 100
+ max_coverage 1000.0
+ max_relative_coverage 1.1 ; bulge_cov < this * not_bulge_cov
+ max_delta 3
+ max_relative_delta 0.1
+ max_number_edges 1000
+ dijkstra_vertex_limit 3000
+ parallel true
+ buff_size 10000
+ buff_cov_diff 2.
+ buff_cov_rel_diff 0.2
+ min_identity 0.0
+ }
+
+ ; erroneous connections remover:
+ ec
+ {
+ ; ec_lb: max_ec_length = k + ec_lb
+ ; icb: iterative coverage bound
+ ; to_ec_lb: max_ec_length = 2*tip_length(to_ec_lb) - 1
+ condition "{ to_ec_lb 5, icb auto }"
+ ; condition "{ ec_lb 9, icb 40.0 }"
+ }
+
+ dead_end {
+ enabled false
+ condition ""
+ }
+
+ ; ==== POST-SIMPLIFICATION ====
+
+ ; relative coverage erroneous connections remover:
+ rcec
+ {
+ enabled false
+ rcec_lb 30
+ rcec_cb 0.5
+ }
+
+ ; relative coverage erroneous component remover:
+ rcc
+ {
+ enabled false
+ coverage_gap 5.
+ max_length_coeff 2.0
+ max_length_with_tips_coeff 3.0
+ max_vertex_cnt 30
+ max_ec_length_coefficient 30
+ max_coverage_coeff 2.0
+ }
+
+ ; relative edge disconnector:
+ red
+ {
+ enabled false
+ diff_mult 20.
+ edge_sum 10000
+ unconditional_diff_mult 0. ; 0. to disable
+ }
+
+ ; final tip clipper:
+ final_tc
+ {
+ condition ""
+ }
+
+ ; final bulge remover:
+ final_br
+ {
+ enabled false
+ main_iteration_only false
+ max_bulge_length_coefficient 3. ; max_bulge_length = max_bulge_length_coefficient * k
+ max_additive_length_coefficient 100
+ max_coverage 1000.0
+ max_relative_coverage 1.1 ; bulge_cov < this * not_bulge_cov
+ max_delta 3
+ max_relative_delta 0.1
+ max_number_edges 1000
+ dijkstra_vertex_limit 3000
+ parallel true
+ buff_size 10000
+ buff_cov_diff 2.
+ buff_cov_rel_diff 0.2
+ min_identity 0.0
+ }
+
+ ; subspecies bulge remover:
+ subspecies_br
+ {
+ enabled false
+ main_iteration_only false
+ max_bulge_length_coefficient 3. ; max_bulge_length = max_bulge_length_coefficient * k
+ max_additive_length_coefficient 100
+ max_coverage 1000.0
+ max_relative_coverage 1.1 ; bulge_cov < this * not_bulge_cov
+ max_delta 3
+ max_relative_delta 0.1
+ max_number_edges 1000
+ dijkstra_vertex_limit 3000
+ parallel true
+ buff_size 10000
+ buff_cov_diff 2.
+ buff_cov_rel_diff 0.2
+ min_identity 0.0
+ }
+
+
+ ; complex tip clipper
+ complex_tc
+ {
+ enabled false
+ max_relative_coverage -1
+ max_edge_len 100
+ condition "{ tc_lb 3.5 }"
+ }
+
+ ; complex bulge remover
+ cbr
+ {
+ enabled false
+ max_relative_length 5.
+ max_length_difference 5
+ }
+
+ ; isolated edges remover
+ ier
+ {
+ enabled true
+ use_rl_for_max_length false ; max_length will be taken max with read_length
+ use_rl_for_max_length_any_cov true ; use_rl_for_max_length_any_cov will be taken max with read_length
+ max_length 0 ; will be taken max with read_length if option above is set
+ max_coverage 2
+ max_length_any_cov 150 ; will be taken max with read_length if option above is set
+ rl_threshold_increase 0 ; add this value to read length if used, i.e. flags above are set
+ }
+
+ ; hidden ec remover
+ her
+ {
+ enabled false
+ uniqueness_length 1500
+ unreliability_threshold 4
+ relative_threshold 5
+ }
+
+ ; ==== ADVANCED EC REMOVAL ALGO ====
+ ; enable advanced ec removal algo
+ topology_simplif_enabled false
+
+ ; topology based erroneous connection remover
+ tec
+ {
+ max_ec_length_coefficient 55 ; max_ec_length = k + max_ec_length_coefficient
+ uniqueness_length 1500
+ plausibility_length 200
+ }
+
+ ; topology and reliability based erroneous connection remover
+ trec
+ {
+ max_ec_length_coefficient 100 ; max_ec_length = k + max_ec_length_coefficient
+ uniqueness_length 1500
+ unreliable_coverage 2.5
+ }
+
+ ; interstrand erroneous connection remover (thorn remover)
+ isec
+ {
+ max_ec_length_coefficient 100 ; max_ec_length = k + max_ec_length_coefficient
+ uniqueness_length 1500
+ span_distance 15000
+ }
+
+ ; max flow erroneous connection remover
+ mfec
+ {
+ enabled false
+ max_ec_length_coefficient 30 ; max_ec_length = k + max_ec_length_coefficient
+ uniqueness_length 1500
+ plausibility_length 200
+ }
+
+ ; topology tip clipper:
+ ttc
+ {
+ length_coeff 3.5
+ plausibility_length 250
+ uniqueness_length 1500
+ }
+
+}
=====================================
debian/configs/toy.info
=====================================
@@ -0,0 +1,4 @@
+reads toy.yaml
+single_cell false
+; RL 100
+
=====================================
debian/copyright
=====================================
@@ -239,8 +239,7 @@ Files: ext/src/hmmer/libdivsufsort/*
Copyright: 2003-2008 Yuta Mori
License: Expat or X11
-Files: ext/src/hmmer/libdivsufsort/COPYING
- ext/src/hmmer/libdivsufsort/divsufsort.c
+Files: ext/src/hmmer/libdivsufsort/divsufsort.c
ext/src/hmmer/libdivsufsort/divsufsort.h.in
Copyright: 2003-2008 Yuta Mori
License: Expat
=====================================
debian/docs
=====================================
@@ -1 +1,3 @@
README.md
+debian/tests/run-unit-test
+debian/README.test
\ No newline at end of file
=====================================
debian/examples
=====================================
@@ -0,0 +1 @@
+debian/configs
=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
-Tests: run-upstreams-tests
+Tests: run-unit-test
Depends: @,bwa
Restrictions: allow-stderr
=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,21 @@
+#!/bin/bash
+set -e
+
+pkg=spades
+
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+ # shellcheck disable=SC2064
+ trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"/configs
+
+spades --test
+coronaspades --test
+metaspades --test
+plasmidspades --test
+rnaspades --test
=====================================
debian/tests/run-upstreams-tests deleted
=====================================
@@ -1,24 +0,0 @@
-#!/bin/sh
-# autopkgtest check: Run the spades tests for each tool.
-# Author: Sascha Steinbiss <satta at debian.org>
-set -ex
-
-WORKDIR=$(mktemp -d)
-trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM
-cd $WORKDIR
-
-spades --test
-coronaspades --test
-metaspades --test
-plasmidspades --test
-rnaspades --test
-
-# truspades is deprecated in v3.15 and may fail its own test suite.
-if command -v truspades > /dev/null
-then
- if ! truspades --test
- then echo 'W: truspades failed its self-test suite.'
- fi
-else
- echo 'W: truspades is not provided upstream anymore.'
-fi
View it on GitLab: https://salsa.debian.org/med-team/spades/-/compare/dba0a18a8ae6f5b027bebc923ef4c1f97051abdd...dafceccdb6696d3ec132a5ca4af53121bb791ddf
--
View it on GitLab: https://salsa.debian.org/med-team/spades/-/compare/dba0a18a8ae6f5b027bebc923ef4c1f97051abdd...dafceccdb6696d3ec132a5ca4af53121bb791ddf
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