philres ngmlr issues - Githubissues

philres / ngmlr

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations

MIT License

284 stars 41 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

ngmlr stops using cpu and runs infinitely

#109 snm32 opened 3 months ago
0
Update README.md

#108 pesho-ivanov opened 3 months ago
0
comparing large genomes

#107 mrwangyz opened 1 year ago
0
Length of read not equal length of quality values

#106 lunky-zao opened 1 year ago
0
Maybe I find a new bug about RG option

#105 yshcai opened 1 year ago
0
ONT preset values are commented out in code. Why?

#104 TimD1 opened 2 years ago
0
Optional SAM flags

#103 davidvho opened 2 years ago
0
running long jobs

#102 bkallow opened 2 years ago
0
New github release?

#101 nileshpatra opened 2 years ago
0
ilog.h: Added VA_OPT to avoid preprocessor error for VA_ARGS

#100 smoe opened 2 years ago
0
Two typos

#99 smoe opened 2 years ago
0
README.md: consistent spelling of PacBio

#98 smoe closed 2 years ago
0
Segmentation fault

#97 zjwang6 opened 3 years ago
2
Fix for "Signed Integer Overflow in MAPQ"

#96 monsanto-pinheiro closed 2 years ago
3
Signed Integer Overflow in MAPQ Computation

#95 paudano opened 3 years ago
1
segmentation fault using ngmlr 0.2.7

#94 lentil824 opened 3 years ago
13
New user questions

#93 ChristopherRichie opened 3 years ago
0
Error in `ngmlr': double free or corruption (!prev): 0x00002aaed8eeb910

#92 MikeWLloyd opened 3 years ago
4
--bam-fix and cs tag

#91 sjin09 closed 3 years ago
2
Long runtimes (> 3 days) with PacBio data expected or indicative of a problem?

#90 BrianSanderson closed 4 months ago
1
[A SOLUTION TO] => samtools issue : incomplete aux field/truncated file

#89 RemiMaglione opened 3 years ago
2
PacBio: ccs/hifi-reads or filtered subreads?

#88 MrTomRod closed 3 years ago
3
Convex Gap-cost alignment

#87 csuzhang opened 3 years ago
0
NGMLR with samtools 1.10 and 1.11

#86 marcotoffoli opened 3 years ago
5
support for aarch64

#85 t-nojiri opened 3 years ago
1
Indel alignment

#84 shimbalama opened 3 years ago
4
MAPQ of -2147483648 attributed to some reads in samfile (minimum value for an int32)

#83 OmarOakheart opened 3 years ago
1
incomplete aux field and negative mapq?

#82 kautto closed 3 years ago
3
do wrong parameters on -x sequencing technologies affect on alignment results?

#81 holiday10 closed 4 years ago
1
Error when converting sam file to bam

#80 Arfourie closed 4 years ago
3
mapping quality

#79 Wuxy96 opened 4 years ago
1
Soft clipping and read splitting

#78 shimbalama opened 4 years ago
1
possible conflict of encoded reference file

#77 zhixingfeng closed 4 years ago
2
Mapping to repeats leads to deletions with low allele frequency

#76 flashton2003 opened 4 years ago
6
Parse error at line

#75 marcotoffoli opened 4 years ago
19
Read index

#74 shimbalama closed 4 years ago
3
ngmlr version 0.2.8

#73 Wuxy96 closed 4 years ago
2
Tag NM in SAM

#72 Wuxy96 closed 3 years ago
1
differences between ONT and PacBio data

#71 Wuxy96 closed 4 years ago
3
NGMLR very slow on bovine nanopore reads

#70 sdjebali opened 4 years ago
2
PacBio: NGMLR slows from 110 reads-mapped/s to ~1 reads-mapped/s on last million reads

#69 matthale16 opened 4 years ago
0
Reporting >30kb deletion in ONT data

#68 vhfsantos closed 4 years ago
2
Remove last trace of seqan

#67 Millak opened 4 years ago
0
not initialized variable may cause panic in some OS

#66 tsjsdbd opened 4 years ago
2
NGMLR carshes with Aborted (core dumped)`

#65 harmeet1990 opened 4 years ago
0
meaning of no-lowqualitysplit option

#64 LeaveYeah opened 4 years ago
0
calculate the identity of alignments

#63 LinXialab closed 5 years ago
6
task terminated while did't report it

#62 suyanan opened 5 years ago
0
max reported alignments per read?

#61 drfultz opened 5 years ago
1
prevent read splitting/clipping

#60 gvic628 opened 5 years ago
4