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Msyd fix #314

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Merged
lrauschning merged 4 commits into from
Jun 20, 2026
Merged

Msyd fix #314

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60fa197
update conda sha256sum
lrauschning May 20, 2026
f3a9bfd
disable c stdlib warning in lint, seems to be how other cython projec…
lrauschning May 20, 2026
3d6b681
handle single-aln cases in apply_TS
lrauschning Jun 17, 2026
b039923
bump version
lrauschning Jun 19, 2026
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8 changes: 5 additions & 3 deletions conda.recipe/meta.yaml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
{% set version = "1.8.0" %}
{% set sha256 = "915a55840e1283fa61db9507d34af479d1f8a985ed7ab56aa7ccc86716a84780" %}
{% set version = "1.8.1" %}
{% set sha256 = "d36f700264e0636d722c783d15e5722792c460235fccb748fbe73c2910a949c8" %}

package:
name: syri
Expand All @@ -17,8 +17,8 @@ build:

requirements:
build:
- {{ compiler('c') }}
- {{ compiler('cxx') }}
- {{ stdlib("cxx") }}
host:
- python >=3.9
- setuptools
Expand Down Expand Up @@ -51,3 +51,5 @@ about:
extra:
maintainers:
- mnshgl0110
skip-lints:
- compiler_needs_stdlib_c
1 change: 0 additions & 1 deletion pyproject.toml
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Expand Up @@ -23,7 +23,6 @@ dependencies = [
"igraph",
"longestrunsubsequence",
'pysam',
"pulp",
]
dynamic = ["version"]

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2 changes: 1 addition & 1 deletion syri/__init__.py
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@@ -1 +1 @@
__version__ = "1.8.0"
__version__ = "1.8.1"
23 changes: 14 additions & 9 deletions syri/pyxFiles/synsearchFunctions.pyx
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Expand Up @@ -865,20 +865,25 @@ def syri(chromo, threshold, coords, cwdPath, bRT, prefix, tUC, tUP, invgl, tdgl,
########################################################################################################################


cpdef apply_TS(const long[:] astart, const long[:] aend, const long[:] bstart, const long[:] bend, int threshold, int mxgap = 100000000000):
# builds a matrix indicating which alignments are consistent with one another
cpdef apply_TS(const long[:] astart, const long[:] aend, const long[:] bstart, const long[:] bend, int threshold, int mxgap = 100_000_000_000):
cdef:
Py_ssize_t i, j, n = len(astart)
Py_ssize_t i, j # init loop vars
Py_ssize_t n = len(astart)
cpp_map[long, cpp_deq[long]] df
cpp_map[long, cpp_deq[long]].iterator mapit # Leon: unused?
#cpp_map[long, cpp_deq[long]].iterator mapit # Leon: unused?
# handle single aln case
if n == 1:
return {0:[0]}

for i in range(<Py_ssize_t> n):
for j in range(<Py_ssize_t> i+1, <Py_ssize_t> n):
if (astart[j] - aend[i]) < mxgap: # Select only alignments with small gaps
if (astart[j] - astart[i]) > threshold:
if ((astart[j] - aend[i]) < mxgap) and ((bstart[j] - bend[i]) < mxgap): # Select only alignments with small gaps
if (astart[j] - astart[i]) > threshold: # check compatibility on a
if (aend[j] - aend[i]) > threshold:
if (bstart[j] - bend[i]) < mxgap: # Select only alignments with small gaps
if (bstart[j] - bstart[i]) > threshold:
if (bend[j] - bend[i]) > threshold:
df[i].push_back(j)
if (bstart[j] - bstart[i]) > threshold: # check compatibility on b
if (bend[j] - bend[i]) > threshold:
df[i].push_back(j) # add to list of compatible alns
out = {}
for i in range(n):
if df.count(i)== 1:
Expand Down
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