consenrich 0.6.3b1__cp311-cp311-macosx_11_0_arm64.whl → 0.7.1b1__cp311-cp311-macosx_11_0_arm64.whl

consenrich/misc_util.py

@@ -62,6 +62,35 @@ def checkBamFile(bamFile: str) -> bool:
     return has_index
 
 
+def bamsArePairedEnd(bamFiles: List[str], maxReads: int = 1_000) -> List[bool]:
+    """
+    Take a list of BAM files, return a list (bool) indicating whether
+    each BAM contains paired-end reads (True) or only single-end reads (False).
+
+    :param bamFiles: List of paths to BAM files
+    :type bamFiles: List[str]
+    :param maxReads: Maximum number of reads to check in each BAM file
+    :type maxReads: int
+    :return: List of booleans corresponding to each BAM file
+    :rtype: List[bool]
+    """
+
+    results = []
+    for path in bamFiles:
+        paired = False
+        seen = 0
+        with sam.AlignmentFile(path, "rb") as bam:
+            for rec in bam.fetch(until_eof=True):
+                if rec.is_paired:
+                    paired = True
+                    break
+                seen += 1
+                if maxReads is not None and seen >= maxReads:
+                    break
+        results.append(paired)
+    return results
+
+
 def getChromSizesDict(
     sizes_file: str,
     excludeRegex: str = r"^chr[A-Za-z0-9]+$",

{consenrich-0.6.3b1.dist-info → consenrich-0.7.1b1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: consenrich
-Version: 0.6.3b1
+Version: 0.7.1b1
 Summary: Genome-wide estimation of signals hidden in noisy multi-sample HTS datasets
 Author-email: "Nolan H. Hamilton" <nolan.hamilton@unc.edu>
 Requires-Python: >=3.11
@@ -43,8 +43,8 @@ Consenrich is an adaptive linear state estimator that yields genome-wide, uncert
 
 Special emphasis is placed on computational efficiency, model interpretability, and practical utility for downstream tasks that require well-resolved genome-wide signal estimates and uncertainty quantification across samples, such as:
 
-* Consensus detection of open chromatin regions, TF footprints, nucleosome occupancy, histone modification
-* Candidate selection and boundary refinement for differential analyses, fine-mapping, reporter assays, etc.
+* Consensus detection of open chromatin regions, TF binding, histone modification, etc.
+* Candidate prioritization for differential analyses, functional validation, integrative modeling, etc.
 
 [**See the Documentation**](https://nolan-h-hamilton.github.io/Consenrich/) for usage examples, installation details, configuration options, and an API reference.
 

{consenrich-0.6.3b1.dist-info → consenrich-0.7.1b1.dist-info}/RECORD

@@ -1,19 +1,19 @@
-consenrich-0.6.3b1.dist-info/RECORD,,
-consenrich-0.6.3b1.dist-info/WHEEL,sha256=sunMa2yiYbrNLGeMVDqEA0ayyJbHlex7SCn1TZrEq60,136
-consenrich-0.6.3b1.dist-info/entry_points.txt,sha256=EXIGcSTyc16vtPkfHJNs-aaSVoq6Pn5Ev5GeW1JCYn0,58
-consenrich-0.6.3b1.dist-info/top_level.txt,sha256=jsWw8GC11dOKPcdULXk-ggW357CO-vTNW6ssryqa21Q,11
-consenrich-0.6.3b1.dist-info/METADATA,sha256=MAf49unrS7M1GZ0pU2s5TJAk2ZYJ3pJ6nfxlUXiMFm8,2563
-consenrich-0.6.3b1.dist-info/licenses/LICENSE,sha256=w09-aT0LFrH_cL3ShJWz-xusRpbThwTpdmBD08tc8EI,1074
-consenrich/detrorm.py,sha256=aJf4uZy2qgDIFfkOpTPJw2akVZ6H8-K64UZ63C6aZBw,8508
-consenrich/misc_util.py,sha256=SoUCgiON_9dbRbrZQoN2NlitDn6fhOgxe4hBYmWvZaI,2726
+consenrich-0.7.1b1.dist-info/RECORD,,
+consenrich-0.7.1b1.dist-info/WHEEL,sha256=sunMa2yiYbrNLGeMVDqEA0ayyJbHlex7SCn1TZrEq60,136
+consenrich-0.7.1b1.dist-info/entry_points.txt,sha256=EXIGcSTyc16vtPkfHJNs-aaSVoq6Pn5Ev5GeW1JCYn0,58
+consenrich-0.7.1b1.dist-info/top_level.txt,sha256=jsWw8GC11dOKPcdULXk-ggW357CO-vTNW6ssryqa21Q,11
+consenrich-0.7.1b1.dist-info/METADATA,sha256=k4w1b9xjG8desy5lYNQ1Kzsj_HcyFn7nqpgRx5ghcIY,2539
+consenrich-0.7.1b1.dist-info/licenses/LICENSE,sha256=w09-aT0LFrH_cL3ShJWz-xusRpbThwTpdmBD08tc8EI,1074
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+consenrich/misc_util.py,sha256=OIjYvwbkW2SbTNhqFO1LnVFuHJK3syU2M1Vzo2SeLc4,3675
 consenrich/constants.py,sha256=5YdNjeyeR1iGbYJXACpxLFS2xVBoyN9bqC7InXPdqKw,5063
 consenrich/__init__.py,sha256=lg02bx0LdXDIQ7Q-tky01xo0tOXYTcJeXqaCXNSFFyA,320
-consenrich/core.py,sha256=RYRBVNoRCFlOYaD_KHApzIy9CcYIoewPT160o8IlM24,52302
-consenrich/matching.py,sha256=UdZfuoDxeiPLgwtu246rYnNrF4QQRUUeezo5Xcbn_4Y,27725
-consenrich/consenrich.py,sha256=f2ZvuQO5AsSS5oo2vxekMGpeEzLSsee04CKXFknr7FI,35486
-consenrich/cconsenrich.cpython-311-darwin.so,sha256=tlE_iCFWNfkpQQthQrC_y5VJ8Qdg640mw_B-YLvs8YE,392816
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+consenrich/matching.py,sha256=kuzGG9ZuPY2ykCQxlKLnvSfhz9V91Ff2iaWW1uMgE2o,28053
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+consenrich/cconsenrich.cpython-311-darwin.so,sha256=BzEc-OS3aafslJm0Cy7IMWFBpxlI3tc_HnPVbh6Vu9g,392816
 consenrich/cconsenrich.pyx,sha256=Wht-d6sUJ-zma0rNHx4DcAIsooFaSR_BdftjJxCLRv8,32604
-consenrich/cconsenrich.c,sha256=fL1mF_9kyb1rt1Hi4ryX-0FdFwUT-KzYCRS_HCye_Cc,2052512
+consenrich/cconsenrich.c,sha256=FifCjZP6ZQmEv-YH8pnfj4JnfGDC4VCyUovkwiYm0EY,2052512
 consenrich/data/hg19.sizes,sha256=ewnSktA_Ps1BoiU3yeLNaJxJO-taq3uKE4-6JUnly1o,365
 consenrich/data/mm10.sizes,sha256=sgHMQGBr6yEm4hKqeN3auQJdlMX4ZdqDQ23EdDmWedU,320
 consenrich/data/hg38_blacklist.bed,sha256=zbamE4bP5JJT-ivyDp61LjvaI00Wo-vd0oKtFxy_u4E,14940