[med-svn] [Git][med-team/pairtools][upstream] New upstream version 1.1.3
Andreas Tille (@tille)
gitlab at salsa.debian.org
Sat Feb 15 18:38:40 GMT 2025
Andreas Tille pushed to branch upstream at Debian Med / pairtools
Commits:
047dd9ac by Andreas Tille at 2025-02-15T17:43:35+01:00
New upstream version 1.1.3
- - - - -
8 changed files:
- CHANGES.md
- doc/installation.rst
- pairtools/__init__.py
- pairtools/lib/parse.py
- pairtools/lib/select.py
- readthedocs.yml
- tests/data/mock.parse2.sam
- tests/test_parse2.py
Changes:
=====================================
CHANGES.md
=====================================
@@ -1,3 +1,19 @@
+### 1.1.3 (2025-01-31) ###
+
+Bugfixes of parse2:
+- Standartiation of complex pair types: names R1&2 and R1-2 are now uniform in the code.
+This was inconistent before leading to the bugs at the positions assignment for R1&2.
+
+- Walk policies are applied not only to complex walks but also to non-chimeric reads in parse2.
+
+
+Bugfizes of pairtools select:
+- Empty columns at the end of the .pairs file are not truncated anymore.
+
+New tests:
+- parse2 tests for R1&2 and R2 reads (read25/27).
+- parse2 tests for correct flipping (read25/26).
+
### 1.1.2 (2024-12-11) ###
Bugfixes:
=====================================
doc/installation.rst
=====================================
@@ -64,3 +64,17 @@ A few notes on the installation:
get lost after the build.
- Because of the `--no-build-isolation` flag, build does not install build-requires, so you have to
install `cython`, `pysam` and `numpy` manually before the build.
+
+
+Building on MacOS is not fully supported yet, but this tentative solution seems to work:
+
+.. code-block:: bash
+
+ $ pip install build cython pysam numpy delocate
+ $ cd pairtools
+ $ python -m build -n
+ $ DYLD_LIBRARY_PATH=$(python -c 'import pysam, os; print(os.path.dirname(pysam.get_libraries()[0]))') delocate-wheel -v dist/{wheel_name}.whl
+ $ pip install dist/{wheel_name}.whl
+
+Note that you need to change the `{wheel_name}` to the actual name of the wheel file.
+
=====================================
pairtools/__init__.py
=====================================
@@ -10,6 +10,6 @@ CLI tools to process mapped Hi-C data
"""
-__version__ = "1.1.2"
+__version__ = "1.1.3"
# from . import lib
=====================================
pairtools/lib/parse.py
=====================================
@@ -750,13 +750,15 @@ def parse2_read(
)
else:
# If no additional information, we assume each molecule is a single ligation with single unconfirmed pair:
- algn2 = algns2[0]
- if report_orientation == "walk":
- algn2 = flip_orientation(algn2)
- if report_position == "walk":
- algn2 = flip_position(algn2)
pair_index = (1, "R1-2")
- return iter([(algns1[0], algn2, pair_index)]), algns1, algns2
+ algn1, algn2, pair_index = format_pair(
+ algns1[0],
+ algns2[0],
+ pair_index=pair_index,
+ report_position=report_position,
+ report_orientation=report_orientation,
+ )
+ return iter([(algn1, algn2, pair_index)]), algns1, algns2
####################
@@ -1363,12 +1365,12 @@ def format_pair(
elif pair_type == "R1-2":
hic_algn2 = flip_orientation(hic_algn2)
elif report_orientation == "pair":
- if pair_type == "R1" or pair_type == "R1&R2":
+ if pair_type == "R1" or pair_type == "R1&2":
hic_algn2 = flip_orientation(hic_algn2)
elif pair_type == "R2":
hic_algn1 = flip_orientation(hic_algn1)
elif report_orientation == "junction":
- if pair_type == "R1" or pair_type == "R1&R2":
+ if pair_type == "R1" or pair_type == "R1&2":
hic_algn1 = flip_orientation(hic_algn1)
elif pair_type == "R2":
hic_algn2 = flip_orientation(hic_algn2)
@@ -1385,18 +1387,20 @@ def format_pair(
elif pair_type == "R1-2":
hic_algn2 = flip_position(hic_algn2)
elif report_position == "outer":
- if pair_type == "R1" or pair_type == "R1&R2":
+ if pair_type == "R1" or pair_type == "R1&2":
hic_algn2 = flip_position(hic_algn2)
elif pair_type == "R2":
hic_algn1 = flip_position(hic_algn1)
elif report_position == "junction":
- if pair_type == "R1" or pair_type == "R1&R2":
+ if pair_type == "R1" or pair_type == "R1&2":
hic_algn1 = flip_position(hic_algn1)
elif pair_type == "R2":
hic_algn2 = flip_position(hic_algn2)
- else:
+ elif pair_type == "R1-2":
hic_algn1 = flip_position(hic_algn1)
hic_algn2 = flip_position(hic_algn2)
+ else:
+ raise ValueError(f"Unknown pair type: {pair_type}")
return [hic_algn1, hic_algn2, pair_index]
=====================================
pairtools/lib/select.py
=====================================
@@ -76,7 +76,7 @@ def evaluate_stream(
match_func = compile(condition, "<string>", "eval")
for line in headerless_stream:
- COLS = line.rstrip().split(pairsam_format.PAIRSAM_SEP)
+ COLS = line.rstrip('\n').split(pairsam_format.PAIRSAM_SEP)
# Evaluate filtering expression:
filter_passed = eval(match_func)
=====================================
readthedocs.yml
=====================================
@@ -1,18 +1,35 @@
# .readthedocs.yml
+
+# For some reason, readthedocs' platform does not import the installed package (from .../envs/),
+# but instead reads another copy from .../checkouts/. This other copy does not have compiled
+# cython objects and throws and error.
+# To overcome this issue, we had to use a custom job to install pairtools in the editable mode
+# and thus ensure that the cython code is compiled.
+# Another potentially useful trick in the future: setting environmental variables
+# (e.g. PIP_VERBOSE and PIP_NO_BUILD_ISOLATION=false) can control pip's behaviour in
+# the standard install job.
+
+
version: 2
build:
os: ubuntu-22.04
tools:
python: "3.10"
+ jobs:
+ post_create_environment:
+ - pip install numpy cython pysam
+ - pip install --no-build-isolation -e .[doc]
+ - python -c "import pairtools.lib.dedup_cython"
+
+# python:
+# install:
+# - method: pip
+# path: .
+# extra_requirements:
+# - doc
sphinx:
configuration: doc/conf.py
-python:
- install:
- - method: pip
- path: .
- extra_requirements:
- - doc
\ No newline at end of file
=====================================
tests/data/mock.parse2.sam
=====================================
@@ -1,34 +1,34 @@
@SQ SN:chr1 LN:10000
@SQ SN:chr2 LN:10000
@PG ID:mock PN:mock VN:0.0.0 CL:mock
-readid01 65 chr1 10 60 50M chr1 200 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:chr1,10,chr1,200,+,+,UU,1,R1-2
-readid01 129 chr1 200 60 50M chr1 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:chr1,10,chr1,200,+,+,UU,1,R1-2
-readid02 97 chr1 10 60 50M chr1 200 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:chr1,10,chr1,249,+,-,UU,1,R1-2
-readid02 145 chr1 200 60 50M chr1 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:chr1,10,chr1,249,+,-,UU,1,R1-2
-readid03 65 chr1 10 60 1S49M chr1 200 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:chr1,10,chr1,200,+,+,UU,1,R1-2
-readid03 129 chr1 200 60 50M chr1 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:chr1,10,chr1,200,+,+,UU,1,R1-2
-readid04 81 chr1 10 60 49M1S chr1 200 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:chr1,58,chr1,200,-,+,UU,1,R1-2
-readid04 161 chr1 200 60 50M chr1 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:chr1,58,chr1,200,-,+,UU,1,R1-2
-readid05 97 chr1 10 60 50M chr1 200 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:chr1,10,chr1,248,+,-,UU,1,R1-2
-readid05 145 chr1 200 60 1S49M chr1 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:chr1,10,chr1,248,+,-,UU,1,R1-2
-readid06 97 chr1 10 60 50M chr1 200 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:chr1,10,chr1,248,+,-,UU,1,R1-2
-readid06 145 chr1 200 60 49M1S chr1 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:chr1,10,chr1,248,+,-,UU,1,R1-2
-readid07 97 chr1 10 60 50M chr1 200 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:chr1,10,chr1,247,+,-,UU,1,R1-2
-readid07 145 chr1 200 60 1S48M1S chr1 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:chr1,10,chr1,247,+,-,UU,1,R1-2
-readid08 105 chr1 10 60 50M = 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:!,0,chr1,10,-,+,NU,1,R1-2
-readid08 149 * 0 0 * chr1 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:!,0,chr1,10,-,+,NU,1,R1-2
-readid09 85 * 0 0 * chr1 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:!,0,chr1,10,-,+,NU,1,R1-2
-readid09 169 chr1 10 60 50M = 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:!,0,chr1,10,-,+,NU,1,R1-2
+readid01 65 chr1 10 60 50M chr1 200 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:chr1,59,chr1,249,+,+,UU,1,R1-2
+readid01 129 chr1 200 60 50M chr1 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:chr1,59,chr1,249,+,+,UU,1,R1-2
+readid02 97 chr1 10 60 50M chr1 200 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:chr1,59,chr1,200,+,-,UU,1,R1-2
+readid02 145 chr1 200 60 50M chr1 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:chr1,59,chr1,200,+,-,UU,1,R1-2
+readid03 65 chr1 10 60 1S49M chr1 200 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:chr1,58,chr1,249,+,+,UU,1,R1-2
+readid03 129 chr1 200 60 50M chr1 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:chr1,58,chr1,249,+,+,UU,1,R1-2
+readid04 81 chr1 10 60 49M1S chr1 200 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:chr1,10,chr1,249,-,+,UU,1,R1-2
+readid04 161 chr1 200 60 50M chr1 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:chr1,10,chr1,249,-,+,UU,1,R1-2
+readid05 97 chr1 10 60 50M chr1 200 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:chr1,59,chr1,200,+,-,UU,1,R1-2
+readid05 145 chr1 200 60 1S49M chr1 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:chr1,59,chr1,200,+,-,UU,1,R1-2
+readid06 97 chr1 10 60 50M chr1 200 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:chr1,59,chr1,200,+,-,UU,1,R1-2
+readid06 145 chr1 200 60 49M1S chr1 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:chr1,59,chr1,200,+,-,UU,1,R1-2
+readid07 97 chr1 10 60 50M chr1 200 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:chr1,59,chr1,200,+,-,UU,1,R1-2
+readid07 145 chr1 200 60 1S48M1S chr1 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:chr1,59,chr1,200,+,-,UU,1,R1-2
+readid08 105 chr1 10 60 50M = 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:!,0,chr1,59,-,+,NU,1,R1-2
+readid08 149 * 0 0 * chr1 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:!,0,chr1,59,-,+,NU,1,R1-2
+readid09 85 * 0 0 * chr1 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:!,0,chr1,59,-,+,NU,1,R1-2
+readid09 169 chr1 10 60 50M = 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:!,0,chr1,59,-,+,NU,1,R1-2
readid10 77 * 0 0 * * 0 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:!,0,!,0,-,-,NN,1,R1-2
readid10 141 * 0 0 * * 0 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:!,0,!,0,-,-,NN,1,R1-2
readid11 105 chr1 10 0 50M = 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:!,0,!,0,-,-,NM,1,R1-2
readid11 149 * 0 0 * chr1 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:!,0,!,0,-,-,NM,1,R1-2
readid12 85 * 0 0 * chr1 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:!,0,!,0,-,-,NM,1,R1-2
readid12 169 chr1 10 0 50M = 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:!,0,!,0,-,-,NM,1,R1-2
-readid13 65 chr1 10 0 50M chr1 200 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:!,0,chr1,200,-,+,MU,1,R1-2
-readid13 129 chr1 200 60 50M chr1 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:!,0,chr1,200,-,+,MU,1,R1-2
-readid14 65 chr1 10 60 50M chr1 200 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:!,0,chr1,10,-,+,MU,1,R1-2
-readid14 129 chr1 200 0 50M chr1 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:!,0,chr1,10,-,+,MU,1,R1-2
+readid13 65 chr1 10 0 50M chr1 200 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:!,0,chr1,249,-,+,MU,1,R1-2
+readid13 129 chr1 200 60 50M chr1 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:!,0,chr1,249,-,+,MU,1,R1-2
+readid14 65 chr1 10 60 50M chr1 200 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:!,0,chr1,59,-,+,MU,1,R1-2
+readid14 129 chr1 200 0 50M chr1 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:!,0,chr1,59,-,+,MU,1,R1-2
readid15 65 chr1 10 0 50M chr1 200 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:!,0,!,0,-,-,MM,1,R1-2
readid15 129 chr1 200 0 50M chr1 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:!,0,!,0,-,-,MM,1,R1-2
readid16 65 chr1 10 60 25M25S chr1 200 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 SA:Z:chr1,300,-,25M25H,60,0; CT:Z:SIMULATED:chr1,34,chr1,324,+,+,UU,1,R1
@@ -56,3 +56,14 @@ readid22 129 chr1 200 0 50M chr1 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
readid23 129 chr1 200 0 50M chr1 10 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 NM:i:0 CT:Z:SIMULATED:!,0,!,0,-,-,XX,1,R1-2
readid24 65 chr1 10 60 25M25S chr1 200 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 SA:Z:chr1,5300,-,25M25H,60,0; CT:Z:SIMULATED:chr1,34,chr1,5324,+,+,UU,1,R1|!,0,chr1,5300,-,-,NU,2,R1-2
readid24 2129 chr1 5300 60 25M25H chr1 200 0 AAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 CT:Z:SIMULATED:chr1,34,chr1,5324,+,+,UU,1,R1|!,0,chr1,5300,-,-,NU,2,R1-2
+readid25 97 chr1 1 60 36S45M = 1 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 SA:Z:chr1,200,+,38M43S,60,0; CT:Z:SIMULATED:chr1,1,chr1,237,-,+,UU,1,R1&2
+readid25 2145 chr1 200 60 38M43H chr1 1 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 SA:Z:chr1,1,+,36S45M,60,0; CT:Z:SIMULATED:chr1,1,chr1,237,-,+,UU,1,R1&2
+readid25 145 chr1 1 60 168S53M = 1 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 SA:Z:chr1,200,-,132S38M51S,60,0; CT:Z:SIMULATED:chr1,1,chr1,237,-,+,UU,1,R1&2
+readid25 2193 chr1 200 60 132H38M51H chr1 1 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 SA:Z:chr1,1,-,168S53M,60,0; CT:Z:SIMULATED:chr1,1,chr1,237,-,+,UU,1,R1&2
+readid26 97 chr1 200 60 36S45M = 1 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 SA:Z:chr1,1,+,38M43S,60,0; CT:Z:SIMULATED:chr1,38,chr1,200,+,-,UU,1,R1&2
+readid26 2145 chr1 1 60 38M43H chr1 1 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 SA:Z:chr1,200,+,36S45M,60,0; CT:Z:SIMULATED:chr1,38,chr1,200,+,-,UU,1,R1&2
+readid26 145 chr1 200 60 168S53M = 1 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 SA:Z:chr1,1,-,132S38M51S,60,0; CT:Z:SIMULATED:chr1,38,chr1,200,+,-,UU,1,R1&2
+readid26 2193 chr1 1 60 132H38M51H chr1 1 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 SA:Z:chr1,200,-,168S53M,60,0; CT:Z:SIMULATED:chr1,38,chr1,200,1,+,-,UU,1,R1&2
+readid27 97 chr1 128 60 81M = 200 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 CT:Z:SIMULATED:chr1,1,chr1,369,-,+,UU,1,R2
+readid27 145 chr1 200 60 170M51S = 128 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 SA:Z:chr1,1,-,168S53M,60,0; CT:Z:SIMULATED:chr1,1,chr1,369,-,+,UU,1,R2
+readid27 2193 chr1 1 60 168H53M chr1 128 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA NM:i:0 SA:Z:chr1,200,-,170M51S,60,0; CT:Z:SIMULATED:chr1,1,chr1,369,-,+,UU,1,R2
=====================================
tests/test_parse2.py
=====================================
@@ -260,4 +260,4 @@ def test_mock_pysam_parse2_single_end_expand():
print(simulated_pair, prev_id)
print()
- assert assigned_pair == simulated_pair
\ No newline at end of file
+ assert assigned_pair == simulated_pair
View it on GitLab: https://salsa.debian.org/med-team/pairtools/-/commit/047dd9ac08fcda43b73eb45b3187bf6792a5f627
--
View it on GitLab: https://salsa.debian.org/med-team/pairtools/-/commit/047dd9ac08fcda43b73eb45b3187bf6792a5f627
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