ctskennerton/crass issues and pull requests

#103 - Are sockets links established during crass execution?

Issue - State: open - Opened by wanghang7410 11 months ago - 1 comment

#102 - ERROR: parseSeqFiles failed

Issue - State: open - Opened by fanlu-f almost 3 years ago - 1 comment

#101 - FATAL ERROR: parseSeqFiles failed

Issue - State: closed - Opened by maureenbug almost 4 years ago - 8 comments

#100 - question about crass-assembler

Issue - State: closed - Opened by ucassee about 4 years ago - 9 comments

#99 - Multiple .gv files per group?

Issue - State: open - Opened by MeggyC over 4 years ago - 5 comments

#98 - Installation problem during make

Issue - State: closed - Opened by schne236 over 4 years ago - 4 comments

#97 - How to deal with paired-end Illumina reads

Issue - State: closed - Opened by 473021677 over 4 years ago - 1 comment

#96 - Crass compilation error

Issue - State: closed - Opened by Russel88 almost 6 years ago - 7 comments

#95 - Xerces-C Parser headers found bit Parse libraries and parser not found

Issue - State: closed - Opened by dangeles almost 6 years ago - 11 comments

#94 - ./autogen.sh gets hung up

Issue - State: closed - Opened by dangeles almost 6 years ago - 2 comments

#93 - Crass compilation

Issue - State: closed - Opened by 473021677 about 6 years ago - 2 comments

#92 - installation error (Xerces-c)

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

#91 - quick Q of Coverage and spid

Issue - State: closed - Opened by Ruonan0101 almost 7 years ago - 2 comments

#90 - Make error

Issue - State: closed - Opened by Ruonan0101 almost 7 years ago - 3 comments

#89 - Crass hangs on the patternFinder step

Issue - State: open - Opened by philippmuench about 7 years ago - 9 comments

#88 - crass : [ERROR] Could not open FASTQ <groupfile.fa> for reading.

Issue - State: closed - Opened by josmos over 7 years ago - 2 comments

#87 - v0.3.7 error

Issue - State: closed - Opened by snayfach almost 8 years ago - 1 comment

#86 - Crass installation error

Issue - State: closed - Opened by XiaoqiongGu over 8 years ago - 3 comments

#85 - src: test: Remove reference to test_readholder.cpp

Pull Request - State: open - Opened by wwood over 8 years ago

#84 - fastq processing error

Issue - State: open - Opened by grokkaine over 8 years ago - 1 comment

#83 - Install issue zlib related on gcc/g++ 4.7 and 4.8 on Ubuntu 16.04 LTS

Issue - State: closed - Opened by grokkaine over 8 years ago - 4 comments

#82 - [ERROR]: FATAL ERROR: parseSeqFiles failed

Issue - State: open - Opened by shaman-narayanasamy over 8 years ago - 14 comments

#81 - changing minDR and maxDR give unexpected output

Issue - State: open - Opened by michberr over 8 years ago - 4 comments

#80 - Assembly results: bad interpretation or error?

Issue - State: open - Opened by grokkaine over 8 years ago - 2 comments

#79 - Installation Error

Issue - State: open - Opened by ghoshal almost 9 years ago - 4 comments

#78 - crass-assembly

Issue - State: closed - Opened by lianzhh almost 9 years ago - 1 comment

#77 - crass-assembly

Issue - State: closed - Opened by lianzhh almost 9 years ago

#76 - help exit with 0 not 1

Pull Request - State: closed - Opened by EricDeveaud almost 9 years ago

#75 - Crass throwing an instance of 'std::out_of_range'

Issue - State: closed - Opened by rwolfe45 almost 9 years ago - 5 comments

#74 - Installation error

Issue - State: closed - Opened by shaman-narayanasamy over 9 years ago - 7 comments

#73 - counter overflows when there is too much deluge

Issue - State: closed - Opened by wwood almost 10 years ago - 2 comments

#72 - Crass make failure #'Utils.h' file not found

Issue - State: closed - Opened by fmoyaflores about 10 years ago - 2 comments

#71 - crass make failure

Issue - State: closed - Opened by chriswalls about 10 years ago - 14 comments

#70 - new segmentation fault error

Issue - State: closed - Opened by jungbluth about 10 years ago - 1 comment

#69 - Installation Problem: Cannot find Xerces-c

Issue - State: closed - Opened by shafferm about 11 years ago - 2 comments

#68 - crass-assembler not locating velvet

Issue - State: closed - Opened by shaman-narayanasamy over 11 years ago - 7 comments

#67 - problem with crass-assembly! failed!

Issue - State: closed - Opened by heying340 over 11 years ago - 4 comments

#66 - .log output error Mac OS vs. Ubuntu

Issue - State: closed - Opened by nataliafose almost 12 years ago - 1 comment

#65 - libcrispr install error

Issue - State: closed - Opened by 11xinqi almost 12 years ago - 11 comments

#64 - libcrispr Installation [SOLVED]

Issue - State: closed - Opened by shaman-narayanasamy almost 12 years ago - 13 comments

#63 - libcrispr libraries not found

Issue - State: closed - Opened by nick-youngblut almost 12 years ago - 7 comments

#62 - small tutorial.html fixes

Pull Request - State: closed - Opened by wwood almost 12 years ago

#61 - Substring error

Issue - State: closed - Opened by ctSkennerton about 12 years ago - 6 comments
Labels: defect, priority-high

#61 - Substring error

Issue - State: closed - Opened by ctSkennerton about 12 years ago - 6 comments
Labels: defect, priority-high

#60 - Installation Issues

Issue - State: closed - Opened by sunitj over 12 years ago - 2 comments

#59 - DR bounderies wrong

Issue - State: closed - Opened by ctSkennerton over 12 years ago - 1 comment
Labels: defect

#58 - poor performance with Illumina 150bp reads

Issue - State: closed - Opened by ctSkennerton over 12 years ago
Labels: improvment

#57 - Contigs in crispr file have no spacers

Issue - State: closed - Opened by ctSkennerton almost 13 years ago
Labels: defect

#56 - final DRs too small

Issue - State: closed - Opened by ctSkennerton almost 13 years ago
Labels: defect, priority-high

#55 - mismatch between stored DR and searched DR for singleton finder

Issue - State: closed - Opened by ctSkennerton almost 13 years ago
Labels: defect, priority-high

#54 - Outputted DRs not expanded with --removeHomopolymers

Issue - State: closed - Opened by ctSkennerton almost 13 years ago
Labels: defect, priority-high

#53 - bad alloc in workhorse

Issue - State: closed - Opened by ctSkennerton almost 13 years ago - 1 comment
Labels: defect, priority-high

#52 - outputted fasta files do not match groups reported by crisprtools stat

Issue - State: closed - Opened by ctSkennerton almost 13 years ago
Labels: defect, priority-high

#51 - option removeHomopolymers causing crash

Issue - State: closed - Opened by ctSkennerton almost 13 years ago - 3 comments
Labels: defect, priority-high

#50 - crisprtools extract seg fault

Issue - State: closed - Opened by ctSkennerton almost 13 years ago - 1 comment
Labels: defect

#49 - crisprtools stat inaccurate read count

Issue - State: closed - Opened by ctSkennerton almost 13 years ago - 1 comment
Labels: defect

#48 - crisprtools sanitise does not change associated files

Issue - State: closed - Opened by ctSkennerton almost 13 years ago - 1 comment
Labels: defect, priority-med

#47 - crisprtools stat seg fault

Issue - State: closed - Opened by ctSkennerton almost 13 years ago
Labels: defect, priority-med

#46 - crisprtools sanitise does nothing without options

Issue - State: closed - Opened by ctSkennerton almost 13 years ago
Labels: improvment

#45 - crisprtools extract should print to stdout where possible

Issue - State: closed - Opened by ctSkennerton almost 13 years ago - 1 comment
Labels: improvment

#44 - figure out why nr_repeats misses some reads

Issue - State: closed - Opened by ctSkennerton almost 13 years ago
Labels: defect

#43 - crisprtools stat read number output wrong

Issue - State: closed - Opened by ctSkennerton almost 13 years ago
Labels: defect, priority-med

#42 - Seg fault in EBPR metagenomes

Issue - State: closed - Opened by ctSkennerton almost 13 years ago
Labels: defect, priority-high

#41 - Regression of performance in AMD data

Issue - State: closed - Opened by ctSkennerton almost 13 years ago
Labels: defect, priority-high

#40 - speed improvements

Issue - State: closed - Opened by ctSkennerton almost 13 years ago
Labels: feature add, improvment

#39 - crisprtools rm

Issue - State: closed - Opened by ctSkennerton almost 13 years ago
Labels: improvment, priority-low

#38 - crisprtools stat --header option doesn't work

Issue - State: closed - Opened by ctSkennerton almost 13 years ago
Labels: defect, priority-low

#37 - 32bit build issues

Issue - State: closed - Opened by ctSkennerton almost 13 years ago
Labels: defect, priority-low

#36 - Output files not being written silently

Issue - State: closed - Opened by ctSkennerton almost 13 years ago
Labels: defect, priority-med

#35 - Seg fault for JCVI_SMPL_1103283000005.fa

Issue - State: closed - Opened by ctSkennerton about 13 years ago - 4 comments
Labels: defect, priority-high

#34 - Smith-Waterman alignments going past end of sequence

Issue - State: closed - Opened by ctSkennerton about 13 years ago - 2 comments
Labels: defect, priority-high

#33 - graphviz files can contain no spacers

Issue - State: closed - Opened by ctSkennerton about 13 years ago
Labels: defect, priority-med

#32 - seg fault in graph builder

Issue - State: closed - Opened by ctSkennerton about 13 years ago - 1 comment
Labels: defect, priority-high

#31 - change reads output file name based on format

Issue - State: closed - Opened by ctSkennerton about 13 years ago
Labels: defect, priority-med

#30 - Colour code graph by file

Issue - State: closed - Opened by ctSkennerton about 13 years ago
Labels: feature add, priority-med

#29 - Some direct repeats are not in their laurenized form

Issue - State: closed - Opened by ctSkennerton about 13 years ago
Labels: defect, priority-high

#28 - add full path names into files in the xml file

Issue - State: closed - Opened by ctSkennerton about 13 years ago
Labels: defect, priority-low

#27 - duplication of some groups

Issue - State: closed - Opened by ctSkennerton about 13 years ago - 1 comment
Labels: defect, priority-high

#26 - Unwanted files getting installed

Issue - State: closed - Opened by ctSkennerton about 13 years ago
Labels: defect

#25 - Fix seg fault in Workhorse line 633

Issue - State: closed - Opened by ctSkennerton about 13 years ago
Labels: defect, priority-high

#24 - Determine why nodes in bubble removal have less than 2 edges

Issue - State: closed - Opened by ctSkennerton over 13 years ago - 1 comment
Labels: defect, priority-med

#23 - remove direct repeats from groups if a kmer cannot be placed

Issue - State: closed - Opened by ctSkennerton over 13 years ago
Labels: defect, priority-low

#22 - Put in the key generating functions

Issue - State: closed - Opened by ctSkennerton over 13 years ago
Labels: defect, priority-high

#21 - XML printing should be done with Xerces

Issue - State: closed - Opened by ctSkennerton over 13 years ago
Labels: improvment, priority-low

#20 - flankers need to be properly implemented in the printXML function

Issue - State: closed - Opened by ctSkennerton over 13 years ago
Labels: defect, priority-low

#19 - long 'spacers' need to be annotated as flanking sequences

Issue - State: closed - Opened by ctSkennerton over 13 years ago
Labels: defect, improvment, priority-med

#18 - graphs need more cleaning

Issue - State: closed - Opened by ctSkennerton over 13 years ago
Labels: defect, priority-high

#17 - some group do not get assigned coverage

Issue - State: closed - Opened by ctSkennerton over 13 years ago
Labels: defect, priority-med

#16 - Make .crispr more general format

Issue - State: closed - Opened by ctSkennerton over 13 years ago
Labels: improvment, priority-med

#15 - number of reads is different in output compared to internal representations

Issue - State: closed - Opened by ctSkennerton over 13 years ago - 1 comment
Labels: defect, priority-high

#14 - Segmentation fault WorkHorse:421

Issue - State: closed - Opened by ctSkennerton over 13 years ago - 2 comments
Labels: defect, priority-high

#13 - The specificity needs to be improved

Issue - State: closed - Opened by ctSkennerton over 13 years ago - 1 comment
Labels: feature add, improvment

#12 - contigs are not joined in spacer graph

Issue - State: closed - Opened by ctSkennerton over 13 years ago
Labels: defect, priority-high

#11 - dynamically set value of 'B' in WuManber

Issue - State: closed - Opened by ctSkennerton over 13 years ago
Labels: improvment, priority-low

#10 - add paired end assembly to the AssemblyWrapper

Issue - State: closed - Opened by ctSkennerton over 13 years ago
Labels: feature add, priority-low

#9 - Update readme and man files

Issue - State: closed - Opened by ctSkennerton over 13 years ago
Labels: defect, priority-low

#8 - fix throw calls in AssemblyWrapper and CrassXML

Issue - State: closed - Opened by ctSkennerton over 13 years ago
Labels: defect, priority-med

#7 - CrassXML constructor does not match the dtd

Issue - State: closed - Opened by ctSkennerton over 13 years ago
Labels: defect, priority-high

#6 - bubble not corrected when it begins with a jumping edge

Issue - State: closed - Opened by ctSkennerton over 13 years ago
Labels: defect, priority-med

#5 - reduce memory allocations in libCrispr

Issue - State: closed - Opened by ctSkennerton over 13 years ago
Labels: improvment, priority-med

GitHub / ctskennerton/crass issues and pull requests