torognes/swarm issues and pull requests

#183 - Using SWARM on zOTUs instead of dereplicated sequences?

Issue - State: closed - Opened by nick-dil 3 months ago - 2 comments
Labels: question

#182 - Refactor Bloom filter code

Issue - State: open - Opened by torognes 8 months ago
Labels: enhancement

#181 - correct example in the man

Pull Request - State: closed - Opened by vmikk 10 months ago - 2 comments

#180 - swarm terminates if any sequence in the input fasta file has an N

Issue - State: closed - Opened by killidude 11 months ago - 2 comments
Labels: question

#179 - Option to output cluster member ids/sequence id?

Issue - State: closed - Opened by koh-joshua about 1 year ago - 3 comments
Labels: question

#178 - fastidious boundary applies to the consolidated cluster mass?

Issue - State: closed - Opened by frederic-mahe about 1 year ago - 1 comment
Labels: question

#177 - risk of silent 8-bit unsigned integer overflow in score matrix

Issue - State: closed - Opened by frederic-mahe about 1 year ago - 5 comments
Labels: enhancement, question

#176 - Option to exclude seeds or clusters with low abundance

Issue - State: open - Opened by torognes over 1 year ago - 1 comment
Labels: enhancement

#175 - Seeds not in same order as clusters in output files

Issue - State: closed - Opened by andnischneider almost 2 years ago - 2 comments
Labels: question

#174 - integer division might be one byte too small in some cases

Issue - State: closed - Opened by frederic-mahe almost 2 years ago - 14 comments
Labels: enhancement, question

#173 - Invalid numeric argument for option -t or --threads

Issue - State: closed - Opened by Gian77 about 2 years ago - 8 comments
Labels: enhancement

#172 - uc file question

Issue - State: closed - Opened by dougwyu over 2 years ago - 7 comments
Labels: question

#171 - maximal header length

Issue - State: closed - Opened by frederic-mahe almost 3 years ago - 1 comment
Labels: enhancement

#170 - Refine readme citations

Pull Request - State: closed - Opened by lczech almost 3 years ago - 3 comments

#169 - Compiling fails on Windows

Issue - State: closed - Opened by torognes almost 3 years ago - 3 comments
Labels: enhancement

#168 - OTU table without abundance values

Issue - State: closed - Opened by AshleyZhao20 almost 3 years ago - 6 comments
Labels: question

#167 - Issues with plotting: OTU not found

Issue - State: closed - Opened by naurasd about 3 years ago - 3 comments

#166 - way too many clusters?

Issue - State: closed - Opened by Gian77 about 3 years ago - 7 comments
Labels: question

#165 - Add swarm3 citation

Pull Request - State: closed - Opened by lczech over 3 years ago - 3 comments

#164 - Link to new swarm 3 paper

Issue - State: closed - Opened by lczech over 3 years ago - 3 comments

#163 - documentation: maximal input sequence length

Issue - State: closed - Opened by frederic-mahe over 3 years ago - 9 comments
Labels: enhancement

#162 - table formats for making OTU table from swarm results

Issue - State: closed - Opened by SanniH over 3 years ago - 2 comments
Labels: question

#161 - Roadmap

Issue - State: closed - Opened by frederic-mahe over 3 years ago - 9 comments
Labels: enhancement

#160 - Incorrect results with long sequences, very high gap penalties, and d>1

Issue - State: closed - Opened by torognes almost 4 years ago - 9 comments
Labels: bug

#159 - Installation issues

Issue - State: closed - Opened by naurasd almost 4 years ago - 8 comments
Labels: question

#158 - continuous integration service

Issue - State: closed - Opened by frederic-mahe almost 4 years ago - 2 comments
Labels: enhancement

#157 - swarm 3.0 on conda

Issue - State: closed - Opened by Gian77 about 4 years ago - 3 comments
Labels: enhancement, question

#156 - clustering of huge amount of reads

Issue - State: closed - Opened by mariabernard over 4 years ago - 1 comment
Labels: question

#155 - macros for min() and max()?

Issue - State: closed - Opened by frederic-mahe over 4 years ago - 3 comments
Labels: question

#154 - magic value?

Issue - State: closed - Opened by frederic-mahe over 4 years ago - 2 comments
Labels: question

#153 - restrict -x usage to d > 1

Issue - State: closed - Opened by frederic-mahe almost 5 years ago - 2 comments
Labels: enhancement

#152 - Get rid of CityHash?

Issue - State: closed - Opened by torognes about 5 years ago - 3 comments
Labels: enhancement

#151 - Some helgrind tests fail when swarm is compiled for coverage testing

Issue - State: closed - Opened by torognes about 5 years ago - 6 comments
Labels: enhancement

#150 - more amplicons with -d 2 than -d 1?

Issue - State: closed - Opened by KabitaBaral1 about 5 years ago - 2 comments

#149 - swarm 3.0: cppcheck report (low priority)

Issue - State: closed - Opened by frederic-mahe about 5 years ago - 2 comments
Labels: enhancement

#148 - Empty internal files after running swarm with -d 0

Issue - State: closed - Opened by dcm9123 about 5 years ago - 5 comments

#147 - amplicon sequence reconstruction with swarm?

Issue - State: closed - Opened by KabitaBaral1 about 5 years ago - 4 comments
Labels: question

#146 - code coverage 2: the gnarly cases

Issue - State: closed - Opened by frederic-mahe about 5 years ago - 32 comments
Labels: enhancement

#145 - Does swarm work with nanopore short amplicons?

Issue - State: closed - Opened by dcm9123 about 5 years ago - 3 comments
Labels: question

#144 - code modernization (long-term task, very low priority)

Issue - State: closed - Opened by frederic-mahe about 5 years ago - 1 comment
Labels: enhancement

#143 - code coverage for algod1.cc

Issue - State: closed - Opened by frederic-mahe about 5 years ago - 3 comments
Labels: enhancement

#142 - nw.cc: last lines not triggered by a test

Issue - State: closed - Opened by frederic-mahe about 5 years ago - 4 comments
Labels: enhancement

#141 - db.cc: condition is always true

Issue - State: closed - Opened by frederic-mahe about 5 years ago - 7 comments
Labels: enhancement

#140 - code coverage for db.cc

Issue - State: closed - Opened by frederic-mahe about 5 years ago - 2 comments

#139 - code coverage for derep.cc

Issue - State: closed - Opened by frederic-mahe about 5 years ago - 4 comments
Labels: enhancement

#138 - support ambigous nucleotides N

Issue - State: closed - Opened by sfehrmann about 5 years ago - 2 comments

#137 - swarm 3.0 Floating point exception for bloom-bits values 2, 3 and 4

Issue - State: closed - Opened by frederic-mahe about 5 years ago - 3 comments
Labels: enhancement

#136 - avoid variable shadowing, same naming scheme as other local variables

Pull Request - State: closed - Opened by frederic-mahe about 5 years ago - 1 comment

#135 - Code Quality Benchmark (softwipe)

Issue - State: closed - Opened by frederic-mahe over 5 years ago - 25 comments
Labels: enhancement

#134 - DNA base characters other than ACGT

Issue - State: closed - Opened by kemin711 over 5 years ago - 1 comment

#133 - Sort seeds by total mass before output

Issue - State: closed - Opened by torognes over 5 years ago - 4 comments
Labels: enhancement

#132 - pooled samples?

Issue - State: closed - Opened by dcm9123 over 5 years ago - 1 comment
Labels: question

#131 - abundance values generator?

Issue - State: closed - Opened by dcm9123 over 5 years ago - 2 comments
Labels: question

#130 - Measure code coverage

Issue - State: closed - Opened by frederic-mahe over 5 years ago - 9 comments
Labels: enhancement

#129 - Makefile: add an "install" recipe

Issue - State: closed - Opened by frederic-mahe almost 6 years ago - 7 comments
Labels: enhancement

#128 - Error occur in amplicon_contingency_table.py

Issue - State: closed - Opened by debjitde01 almost 6 years ago - 6 comments
Labels: question

#127 - Fastidious Bloom filter requires more memory than indicated in the help

Issue - State: closed - Opened by frederic-mahe almost 6 years ago - 4 comments
Labels: enhancement

#126 - minor unfreed memory allocation (all swarm versions)

Issue - State: closed - Opened by frederic-mahe almost 6 years ago - 4 comments
Labels: enhancement

#125 - incomplete creation of microvariants (short sequences) in swarm 3.0

Issue - State: closed - Opened by frederic-mahe almost 6 years ago - 24 comments
Labels: enhancement

#124 - small memory leak when using the --log option

Issue - State: closed - Opened by frederic-mahe almost 6 years ago - 2 comments
Labels: enhancement

#123 - memory-allocation error in swarm 3 fastidious

Issue - State: closed - Opened by frederic-mahe almost 6 years ago - 7 comments
Labels: bug

#122 - (not so) small tasks around swarm 3.0

Issue - State: closed - Opened by frederic-mahe almost 6 years ago - 7 comments
Labels: enhancement

#121 - segmentation faults with the zobrist branch

Issue - State: closed - Opened by frederic-mahe almost 6 years ago - 2 comments
Labels: bug

#120 - Benign buffer overflow when parsing fasta sequences

Issue - State: closed - Opened by frederic-mahe almost 6 years ago
Labels: enhancement

#119 - ikos static analyzer

Issue - State: closed - Opened by frederic-mahe almost 6 years ago - 3 comments
Labels: enhancement

#118 - swarm output file

Issue - State: closed - Opened by tilaknayak almost 6 years ago - 3 comments

#117 - Update link in readme

Pull Request - State: closed - Opened by mooreryan about 6 years ago - 1 comment

#116 - Problem with fasta header ???

Issue - State: closed - Opened by davidvilanova about 6 years ago - 8 comments

#115 - Potential vulnerabilities identified by Flawfinder

Issue - State: closed - Opened by frederic-mahe over 6 years ago - 2 comments
Labels: enhancement

#114 - improve groff code

Issue - State: closed - Opened by frederic-mahe over 6 years ago - 1 comment

#113 - Compatibility with old GCC versions?

Issue - State: closed - Opened by frederic-mahe over 6 years ago - 5 comments
Labels: question

#112 - Compilation warnings with the new GCC 8.0

Issue - State: closed - Opened by frederic-mahe over 6 years ago - 2 comments
Labels: enhancement

#111 - Can you update bioconda with latest ?

Issue - State: closed - Opened by davidvilanova almost 7 years ago - 2 comments
Labels: question

#110 - Swarm does not start clustering in rare cases

Issue - State: closed - Opened by torognes almost 7 years ago - 9 comments
Labels: bug

#109 - segmentation fault error when using swarm with -d 1

Issue - State: closed - Opened by mariabernard about 7 years ago - 8 comments
Labels: bug

#108 - Wrong cluster id in the uc output

Issue - State: closed - Opened by yoann-dufresne about 7 years ago - 10 comments
Labels: bug

#107 - Port Swarm to other platforms

Issue - State: closed - Opened by torognes over 7 years ago - 11 comments
Labels: enhancement

#106 - bug in -w output when using the -a option

Issue - State: closed - Opened by frederic-mahe over 7 years ago - 1 comment
Labels: bug

#105 - Swarm doesn't exit when run without any inputs

Issue - State: closed - Opened by sariya over 7 years ago - 8 comments
Labels: enhancement

#104 - static analysis of swarm's C++ code (cppcheck)

Issue - State: closed - Opened by frederic-mahe over 7 years ago - 12 comments
Labels: enhancement

#102 - bug in abundance value parsing?

Issue - State: closed - Opened by frederic-mahe over 7 years ago - 8 comments
Labels: enhancement

#101 - How to handle duplicated parameters or options?

Issue - State: closed - Opened by frederic-mahe over 7 years ago - 5 comments
Labels: enhancement

#100 - Error message "‘asprintf’ was not declared in this scope" when compiling in Cygwin

Issue - State: closed - Opened by MVEverett over 7 years ago - 7 comments
Labels: enhancement

#97 - Visualize swarms for d>1

Issue - State: closed - Opened by steph43 almost 8 years ago - 5 comments
Labels: question

#92 - Put the cluster seed identifier in the --seeds output

Issue - State: closed - Opened by a1an77 almost 8 years ago - 2 comments

#91 - Remove abundance from identifiers in output file

Issue - State: closed - Opened by a1an77 almost 8 years ago - 2 comments

#90 - Abundance annotation not recognised

Issue - State: closed - Opened by a1an77 almost 8 years ago - 8 comments
Labels: enhancement

#89 - Develop a swarm-plugin for Qiime 2

Issue - State: open - Opened by frederic-mahe about 8 years ago - 10 comments
Labels: enhancement

#88 - average pairwise distances of each OTU

Issue - State: closed - Opened by ranocchia4 about 8 years ago - 3 comments

#86 - Add support for unseekable pipes

Issue - State: closed - Opened by frederic-mahe about 8 years ago - 1 comment
Labels: enhancement

#82 - Change output sequences to upper case

Issue - State: closed - Opened by torognes over 8 years ago - 3 comments
Labels: enhancement

#80 - Residual variability in swarm clustering results

Issue - State: closed - Opened by frederic-mahe over 8 years ago - 1 comment
Labels: enhancement

#79 - Segmentation fault on empty sequences

Issue - State: closed - Opened by frederic-mahe over 8 years ago - 2 comments
Labels: enhancement

#78 - In rare cases Swarm does not terminate properly

Issue - State: closed - Opened by torognes over 8 years ago - 2 comments
Labels: bug

#77 - Sanitize input options

Issue - State: closed - Opened by torognes over 8 years ago - 3 comments
Labels: enhancement

#76 - Control the range of `d` values

Issue - State: closed - Opened by frederic-mahe over 8 years ago - 2 comments
Labels: enhancement

#68 - control number of generations, for the iterative growth process

Issue - State: closed - Opened by nikosdarzentas almost 9 years ago - 4 comments
Labels: enhancement

#65 - Check that all input sequences are unique

Issue - State: closed - Opened by torognes about 9 years ago - 2 comments
Labels: enhancement

#56 - Clustering with d = 1 and replicates

Issue - State: closed - Opened by trebor-m over 9 years ago - 6 comments
Labels: enhancement

#55 - Complete integration of the fastidious option?

Issue - State: closed - Opened by frederic-mahe over 9 years ago - 7 comments
Labels: enhancement

GitHub / torognes/swarm issues and pull requests