open2c pairtools issues

open2c / pairtools

Extract 3D contacts (.pairs) from sequencing alignments

MIT License

104 stars 32 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Q: parse, are secondary/supplementary reads needed?

#74 keiranmraine closed 5 years ago
2
Assignment of fragment in restrict passed the first fragment.

#73 zhqu1148980644 closed 2 years ago
3
pairtools sort not parallelizing

#72 SooLee closed 8 months ago
2
VisibleDeprecationWarning

#71 zhqu1148980644 closed 2 years ago
3
duplicate the data processing history (currently stored in @PG fields) in #command fields of the .pairs header

#70 golobor closed 2 years ago
1
Add frequency filtering for single cell Hi-C

#69 hbbrandao closed 6 years ago
0
Fragment-level analysis

#68 Phlya opened 6 years ago
41
add extra pair-related annotation to bams, which would allow to restore .pairs from annotated bams

#67 golobor opened 6 years ago
0
pairsamtools subsampling [new tool, enhancement]

#66 sergpolly closed 2 years ago
5
throw an readable error message upon encountering an unpaired sam entry

#65 golobor opened 6 years ago
2
semantic confusion in stats

#64 sergpolly opened 6 years ago
2
rawline vs stripline, little clean up

#63 sergpolly closed 6 years ago
0
bug fix: split stripped lines in dedup

#62 sergpolly closed 6 years ago
0
merge without arguments

#61 hakanozadam closed 2 years ago
1
Versioning Pairsamtools

#60 hakanozadam closed 6 years ago
1
optical dedup stats

#59 sergpolly closed 2 years ago
20
Dedup stats

#58 sergpolly closed 6 years ago
2
stats API updated: algn=chr,pos,strand

#57 sergpolly closed 6 years ago
0
calculate Pc(s) in stats

#56 golobor closed 2 years ago
4
adding stats to dedup

#55 sergpolly closed 6 years ago
4
add non-additive stat summaries to dedup/stats: complexity estimation, cis/total, ...

#54 golobor closed 2 years ago
5
added dedup category to stats

#53 sergpolly closed 7 years ago
1
New stat parse

#52 sergpolly closed 7 years ago
5
add tests for compression/decompression

#51 golobor opened 7 years ago
2
in all pairsamtools, have a unified way to provide/override column indices and the separator

#50 golobor closed 2 years ago
1
new get_header returns remainder of instream

#49 sergpolly closed 7 years ago
1
make auto_open default to stdin/stdout when path evaluates to False

#48 golobor closed 2 years ago
1
use line.strip to avoid bugs

#47 sergpolly closed 7 years ago
0
use line.rstrip() to avoid bugs

#46 sergpolly closed 7 years ago
1
line profile dedup

#45 golobor closed 7 years ago
1
add an option to use other compressors for input/output (lz4, etc)

#44 golobor closed 7 years ago
2
many scaffolds issue fix

#43 sergpolly closed 7 years ago
0
Trim column list in header after split

#42 nvictus closed 7 years ago
1
enable optional reporting of 5' alignments for non-rescuable chimeras

#41 golobor closed 7 years ago
1
dedup should check that the read pairs are dedupped and do not contain unmapped reads

#40 golobor closed 7 years ago
1
`parse_sort` takes forever when reads mapped to scaffold

#39 sergpolly closed 7 years ago
5
pairsamtools merge single file no action?

#38 sergpolly closed 7 years ago
1
merge options expanded with threads and batches

#37 sergpolly closed 7 years ago
1
Replace base exceptions with specialized ones

#36 nvictus closed 7 years ago
0
add a test for the example_pipeline

#35 golobor opened 7 years ago
1
default to bgzip if pbgzip is absent

#34 golobor closed 4 years ago
0
parse throws an error when a chromosome is present in the chromsizes, but not in the bwa index (== sam header).

#33 golobor closed 7 years ago
1
pairsamtools merge fails when symbolic links are provided as an input

#32 sergpolly closed 7 years ago
2
split drops all columns following the SAM columns

#31 golobor closed 7 years ago
1
in parse, add other options to store (CIGAR, genomic span, NM, AS, XA, etc)

#30 golobor closed 6 years ago
1
In merge,change the default number of threads per infile to 1

#29 golobor closed 7 years ago
1
Flip chromosomes in parse according to semantic order #27

#28 nvictus closed 7 years ago
1
in parse, flip pairs according to the semantic order, provided via a chrom.sizes file

#27 golobor closed 7 years ago
1
add mapq filters, possibly at the later stage

#26 golobor closed 7 years ago
1
Drop_seq corrupts Sam entries

#25 golobor closed 7 years ago
1

Previous Next