jts sga issues - Githubissues

jts / sga

de novo sequence assembler using string graphs

http://genome.cshlp.org/content/22/3/549

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issues

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Inconsistent default value for sga assemble -l

#169 Griffan opened 1 year ago
0
graph-concordance documentation unclear

#168 d-cameron closed 2 years ago
2
sga-preqc-report.py Unable to parse the pattern

#167 Sven-Winter opened 3 years ago
0
sga preqc findSingleCopyPeak finds the wrong peak

#166 melop closed 3 years ago
3
running problems with graph-diff

#165 MingjingKang opened 4 years ago
0
installation problem with google-sparsehash

#164 AndreaQ7 opened 4 years ago
5
OverlapProcess.h Missing

#163 cgroza opened 4 years ago
0
substring remaining after rmdup

#162 bvalot closed 4 years ago
3
index for large .fastq file

#161 sunsac opened 4 years ago
0
Inconsistent format representation for assembly graph edges

#160 anuradhawick opened 4 years ago
1
multithread for samtools sort in sga-align, and fix devision by zero when bootstrap fails in sga-astat

#159 cihga39871 closed 5 years ago
0
Python 2 is end of life on 2020-01-01

#158 mr-c opened 5 years ago
1
How to query occurrences of a sequence in sai and rsai ?

#157 kounkou opened 5 years ago
0
configure forces -std=c++98 but that should be moved to relevant Makefiles or sga code adjusted

#156 mmokrejs opened 5 years ago
6
compilation errors with std::__cxx11

#155 lwl1112 closed 5 years ago
3
error while loading shared libraries: libbamtools.so.2.5.1

#154 benliu5085 closed 5 years ago
2
sga-astat module not found

#153 pnatsi opened 5 years ago
0
Update link for google sparse hash library in README

#152 chris-rands closed 6 years ago
1
celegans.pe file not found

#151 pursue9190 closed 6 years ago
12
Like PR #123, use samtools >=1 `sort` format in sga-align script

#150 kastman closed 6 years ago
0
bug fixed for samtools sort

#149 A-Tsai closed 6 years ago
2
Fix error: call to 'abs' is ambiguous

#148 sjackman closed 6 years ago
2
Try to automatically convert from CIGARs v1.4 to v1.3 format

#147 mmokrejs opened 6 years ago
0
Support multiple input SAM/BAM files (v2)

#146 mmokrejs opened 6 years ago
0
Fix typo in INVERSESUFFIXARRAH_H

#145 mmokrejs opened 6 years ago
0
Support multiple input SAM/BAM files

#144 mmokrejs closed 6 years ago
0
sga-bam2de.pl: Use DistanceEst -l30

#143 sjackman closed 6 years ago
3
sga-bam2de.pl returns empty .de file

#142 flopezo closed 6 years ago
3
Error at `make`: VariantIndex.cpp:89:16: error: call to 'abs' is ambiguous

#141 evanbiederstedt closed 6 years ago
13
Blank sections in preqc results

#140 genes-and-genomes closed 7 years ago
1
Version of SGA used for PCAWG Pilot 63 callsets - probabilistic version

#139 ljdursi closed 7 years ago
0
preqc 'variant branches in k-de Bruijn graph' no y-axis title

#138 nottwy opened 7 years ago
0
CFFLAGS & CXXFAGS

#137 nottwy opened 7 years ago
0
Error: Duplicate read ID - sga-bam2de.pl

#136 a-lud opened 7 years ago
2
sga scaffolding and mate-pair orientation

#135 edu3716 opened 7 years ago
0
sga rmdup vs sga filter --no-kmer-check.

#134 yeban opened 7 years ago
0
GCC-6: WARNING unordered_map: present but cannot be compiled

#133 ppericard opened 7 years ago
1
sga assemble reaches edge limit

#132 johnomics closed 7 years ago
2
sga index segfault with large values of -d

#131 sjackman opened 8 years ago
11
configure issues

#130 irenatfh opened 8 years ago
8
fastq files produced by 'sga correct' not always match the length of the reads

#129 mictadlo opened 8 years ago
0
collect2: error: ld returned 1 exit status

#128 mictadlo closed 8 years ago
3
pre-process

#127 hermeseduardo closed 8 years ago
2
set language standard

#126 mateidavid closed 8 years ago
3
scaffold2fasta: Assertion `expectedOverlap < (int)contigString.length()' failed

#125 sjackman opened 8 years ago
18
DistanceEst --mean

#124 sjackman opened 8 years ago
0
sga-bam2de.pl: Fix samtools sort for samtools 1.3

#123 sjackman closed 8 years ago
3
0.10.14 compilation error

#122 wookietreiber closed 8 years ago
4
sga-align: prepareReads: Cannot parse record

#121 sjackman opened 8 years ago
5
error: use of undeclared identifier 'omp_set_num_threads'

#120 sjackman closed 8 years ago
4