secastel phaser issues - Githubissues

secastel / phaser

phasing and Allele Specific Expression from RNA-seq

GNU General Public License v3.0

107 stars 37 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Subprocess now checks call return values

#36 agraubert closed 7 years ago
0
Replaced usage of quit() with sys.exit(1)

#35 agraubert closed 7 years ago
1
Summed DNA and RNA counts in allelic_counts output file?

#34 freerkvandijk closed 4 years ago
5
phaser_gene_ae only compatible with v1.0.0+, I'm using v1.0.0

#33 npklein closed 7 years ago
1
Phaser assigns incorrect SNVs to genes

#32 GrantHov closed 4 years ago
11
phASER based replacement for allelecounter?

#31 JohnMCMa closed 7 years ago
1
Confidence estimate for phased state between two adjacent site within a HaplotypeBlock?

#30 everestial closed 4 years ago
8
Ask the use of some of the problems encountered

#29 clsteam opened 7 years ago
11
phaser can phase indel ?

#28 zeronot closed 7 years ago
3
OSError: [Errno 12] Cannot allocate memory

#27 paulhager closed 7 years ago
3
Improve phased GT in F1 hybrids using partially phased data (PG) generated using pHASER

#26 everestial closed 4 years ago
1
separate read counts from multiple bam files from one individual/importance of pre-phasing?

#25 mce1 closed 4 years ago
6
Possible problem with the update of the tags in the FORMAT field

#24 everestial closed 7 years ago
2
error running phaser, sorry...

#23 evigorito closed 7 years ago
6
Several possible improvements recommendation for pHASER.

#22 everestial closed 4 years ago
4
Allow using comma-separated list of values for --paired_end (similar to --isize and --mapq)

#21 trgaleev closed 7 years ago
0
Haplotype phase of the homozygous allele

#20 everestial closed 4 years ago
17
Phaser limited to maximum two haplotypes per contig?

#19 mscharmann closed 7 years ago
3
"|" pipe symbol in contig /chromosome ID causes crash: Solution

#18 mscharmann closed 7 years ago
1
crash in subprocess.py: OSError: [Errno 7] Argument list too long

#17 mscharmann closed 7 years ago
0
There is a problem connecting setup.py with cython module in the updated version of phaser.r.

#16 everestial closed 7 years ago
8
unsupported operand type(s) for +=: 'int' and 'str'

#15 colindaven closed 7 years ago
9
Fix interpretation of "H" CIGAR operator

#14 marcelm closed 7 years ago
0
Fix: Parse AS tag only when string starts with "AS:"

#13 marcelm closed 8 years ago
0
Add the PS or HP tag to the format field, enable pipe in GT field

#12 everestial closed 7 years ago
2
Typo

#11 colindaven closed 8 years ago
1
Fixed two bugs

#10 freerkvandijk closed 8 years ago
0
Phasing multiple samples in the same VCF file at the same time

#9 npklein closed 8 years ago
1
Add a more informative error message when there is no = separated dat…

#8 npklein closed 7 years ago
0
--chr option, crashing and a possible bug

#7 colindaven closed 8 years ago
11
UnboundLocalError local variable 'sample_column' referenced before assignment

#6 colindaven closed 8 years ago
3
Pseudogenomes

#5 colindaven closed 8 years ago
1
stop processing if there are no het variants

#4 inti closed 8 years ago
3
ignoring variants without PASS flag

#3 inti closed 8 years ago
1
add required argument to required options

#2 npklein closed 8 years ago
0
License?

#1 colindaven closed 8 years ago
1