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base repository: open2c/pairtools
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base: v1.1.2
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head repository: open2c/pairtools
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compare: master
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  • 16 commits
  • 8 files changed
  • 2 contributors

Commits on Dec 11, 2024

  1. Update installation.rst

    golobor authored Dec 11, 2024
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Commits on Dec 17, 2024

  1. Update readthedocs.yml

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  5. Update readthedocs.yml (#259)

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Commits on Dec 18, 2024

  1. Update readthedocs.yml

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Commits on Jan 10, 2025

  1. Broken 'select' evaluation if last columns happen to be empty; fixed.

    agalitsyna committed Jan 10, 2025
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Commits on Jan 14, 2025

  1. R1&2 in parse pair type substituted with R1&R2 everywhere in the code

    agalitsyna committed Jan 14, 2025
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Commits on Jan 15, 2025

  1. - behavior for non-chimeric reads in parse2 is now aligned with those…

    … for parse
    
    - parse2 tests changed for R1-2 pairs
    - R1&R2 is renamed to shorter R1&2 everywhere in the code of `parse.py`
    agalitsyna committed Jan 15, 2025
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Commits on Jan 20, 2025

  1. Parse2 tests for R1&2 and R2 reads (read25-read27). read25/26 is a pa…

    …ir testing correctness of flip.
    agalitsyna committed Jan 20, 2025
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Commits on Jan 31, 2025

  1. v1.1.3 pre-release

    agalitsyna committed Jan 31, 2025
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Showing with 104 additions and 42 deletions.
  1. +16 −0 CHANGES.md
  2. +14 −0 doc/installation.rst
  3. +1 −1 pairtools/__init__.py
  4. +15 −11 pairtools/lib/parse.py
  5. +1 −1 pairtools/lib/select.py
  6. +23 −6 readthedocs.yml
  7. +33 −22 tests/data/mock.parse2.sam
  8. +1 −1 tests/test_parse2.py
16 changes: 16 additions & 0 deletions CHANGES.md
Original file line number Diff line number Diff line change
@@ -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:
14 changes: 14 additions & 0 deletions doc/installation.rst
Original file line number Diff line number Diff line change
@@ -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.

2 changes: 1 addition & 1 deletion pairtools/__init__.py
Original file line number Diff line number Diff line change
@@ -10,6 +10,6 @@
"""

__version__ = "1.1.2"
__version__ = "1.1.3"

# from . import lib
26 changes: 15 additions & 11 deletions pairtools/lib/parse.py
Original file line number Diff line number Diff line change
@@ -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]

2 changes: 1 addition & 1 deletion pairtools/lib/select.py
Original file line number Diff line number Diff line change
@@ -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)
29 changes: 23 additions & 6 deletions readthedocs.yml
Original file line number Diff line number Diff line change
@@ -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
55 changes: 33 additions & 22 deletions tests/data/mock.parse2.sam
Original file line number Diff line number Diff line change
@@ -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
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