alimanfoo/pysamstats
A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.
Python
Issues
- 0
AttributeError: module 'pysam.libcalignmentfile' has no attribute 'IteratorColumnAll'
#157 opened by mmnascimento - 0
PileupColumn.get_query_positions() behavior differs from PileupRead.query_position
#155 opened by jkoubele - 2
Fix for pysam 0.16
#125 opened by alimanfoo - 3
RuntimeWarning: pysam.libcalignedsegment.PileupColumn size changed, may indicate binary incompatibility. Expected 72 from C header, got 88 from PyObject
#112 opened by Nilad - 0
calling long insertion
#142 opened by rsuseno2907 - 1
Running pysamstats with input from /tmp
#135 opened by stewalsh04 - 1
where to download pysamstats license?
#132 opened by N-damo - 0
Replacing assertions with explicit error messages
#127 opened by fedarko - 2
compatibility with python 3.9
#122 opened by gtonkinhill - 3
ValueError: no index available for pileup
#119 opened by 544728460 - 1
Pysamstats: supplementary alignments
#116 opened by martina811 - 6
[Installation issue] _frozen_importlib:219: RuntimeWarning: pysam.libcalignedsegment.PileupColumn size changed, may indicate binary incompatibility. Expected 72 from C header, got 88 from PyObject
#105 opened by matthpich - 0
[How to use] Can pysamstats accept multiple coordinate parameters at the same time?
#108 opened by b-niu - 2
- 0
- 5
error of pysamstats while using python2.7.14
#83 opened by douym - 6
pysam.libchtslib.HTSFile has the wrong size
#94 opened by MeHelmy - 2
Spliced reads being counted as deletions
#65 opened by saldit - 2
- 6
Counting overlapping read-pairs
#98 opened by madsheilskov - 3
Include duplicate reads for pileup
#91 opened by andurill - 4
v1.1 release plan
#85 opened by alimanfoo - 3
loading variation: dtype restrictions
#72 opened by bramverhelst - 1
Add some data fixture to test for changes to results compare to previous versions
#79 opened by hardingnj - 2
- 3
ImportError: No module named opt
#95 opened by lybird300 - 3
Pysam >0.13 doesn't contain samfile_util.h
#75 opened by owainkenwayucl - 1
Carriage return appended to lines
#92 opened by dariober - 1
pysamstats/opt.pyx
#89 opened by worker000000 - 0
- 2
PIP inconsistency in update
#69 opened by bramverhelst - 3
Ignore masked regions
#80 opened by KristinaGagalova - 2
pip install not working
#84 opened by andersgs - 4
Pysam >= 0.12
#82 opened by florealcab - 10
- 3
- 1
Install issue
#71 opened by yasinkaymaz - 5
- 2
specify multiple regions by file (e.g. bed)
#64 opened by madsheilskov - 5
- 2
base-quality threshold
#53 opened by frabanal - 1
Upgrade to pysam 0.10.0
#62 opened by alimanfoo - 2
- 2
Rounding rms values
#57 opened by bramslabbinck - 2
Option to calculate statistics against read position instead of genome position
#63 opened by astewart-twist - 5
Consensus variation stats for paired end?
#60 opened by astewart-twist - 3
- 1
pysamstats Docker image
#58 opened by fjukstad - 3
- 2
Substitutions count
#55 opened by mberacochea