COMBINE-lab pufferfish issues

COMBINE-lab / pufferfish

An efficient index for the colored, compacted, de Bruijn graph

GNU General Public License v3.0

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issues

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Fails to compile on IBM Power architecture (ppc64le)

#47 jblachly opened 9 months ago
0
can't install pufferfish

#46 hungmai1984 opened 9 months ago
0
Create and query an index of many human genomes?

#45 jeremymsimon opened 1 year ago
0
Cedar segfaults with SAM files

#44 hermidalc opened 1 year ago
1
Would Pufferfish index and align be more efficient if I merged each genome into a single contig and FASTA entry per genome?

#43 hermidalc closed 1 year ago
1
PuffAligner significantly slower at mapping and thread usage is much less than specified when running with `--compressedOutput`

#42 hermidalc opened 1 year ago
1
Align command fails or shows help when options aren't in a specific order

#41 hermidalc closed 1 year ago
1
Output unmapped reads

#40 hermidalc opened 1 year ago
0
Parallelize fixFasta

#39 hermidalc opened 1 year ago
0
xz-5.2.2.tar.gz: FAILED

#38 mmpust closed 1 year ago
2
Pufferfish index decoy option fixFasta doesn't recognize FASTA header(s) and fails

#37 hermidalc closed 1 year ago
2
Pufferfish index `--decoys <decoy_list>` option doesn't tell you how to provide a list of FASTA files

#36 hermidalc closed 1 year ago
3
Add description to help that pufferfish index supports gzipped FASTA reference file

#35 hermidalc opened 1 year ago
0
Pufferfish doesn't build within a conda environment (which has all the prerequisites) due to failed build of tslib from SeqLib

#34 hermidalc opened 2 years ago
9
No executable after installing

#32 HenryYihengXu closed 2 years ago
1
[Compile error] cannot open output file cedar: Is a directory

#31 enricorox opened 2 years ago
0
Puffaligner fasta file

#30 nayeon1994 closed 2 years ago
1
Please consider converting ExternalProject_Add to git submodules

#29 yurivict opened 2 years ago
0
kquery, missing command

#28 chklopp closed 2 years ago
28
installing without root

#27 ksahlin opened 2 years ago
13
Built-in FindTBB.cmake fails to find OpenTBB-2021.3.0

#26 yurivict closed 2 years ago
3
Implementation of soft-clipping and CIGAR computation

#25 haghshenas opened 3 years ago
2
Compact_vector.hpp deserialize in read-only shared mmap.

#24 gmarcais closed 3 years ago
0
Puffaligner doesn't map read pairs to different references

#23 apcamargo opened 3 years ago
2
[Question] Effect of the 'genomicReads' parameter

#22 apcamargo opened 3 years ago
1
[Suggestion] Allow output to stdout

#21 apcamargo opened 3 years ago
2
Clarify usage for genome alignment

#20 ssadedin opened 3 years ago
2
Support interleaved paired end FASTQs

#19 nh13 opened 3 years ago
1
Improve the help message, remove duplicate option descriptions, and get clarify options with the same flag

#18 nh13 opened 3 years ago
2
Align without the "-o" option should just output to standard output

#17 nh13 opened 3 years ago
1
Cigar integration

#16 mohsenzakeri closed 4 years ago
0
make install does not work, pufferfish binary segfaults

#15 mathog opened 4 years ago
20
FindJemalloc.cmake does not work on CentOS 8

#14 mathog opened 4 years ago
0
Portable cpuRelax

#13 mr-c closed 4 years ago
1
Building an index using `salmon index` seems stuck at twopaco step

#12 dombraccia closed 4 years ago
2
indexing tsvs

#11 k3yavi closed 4 years ago
1
Create cpp.yml

#10 rob-p closed 4 years ago
0
PackedContigInfoVec

#9 rob-p closed 4 years ago
0
"Index requested greater than vector's size" when loading pufferfish index using salmon v1.0

#8 mdshw5 opened 4 years ago
22
Pufferfish output files

#7 lutzkaro closed 4 years ago
0
Holy build for sharing binary

#6 k3yavi closed 5 years ago
4
fixfasta binary

#5 genomax closed 5 years ago
6
Pufferfish Dependency: Need Help

#4 ruhulsbu closed 4 years ago
1
pufferfish for assembly

#3 SilasK closed 4 years ago
1
compiling version of kraken dump

#2 k3yavi closed 5 years ago
0
Make develop at parity with master

#1 rob-p closed 6 years ago
0