fix no prealignment logic; see #142

databio · Jul 13, 2020 · 10e75d1 · 10e75d1
1 parent 067d935
commit 10e75d1
Show file tree

Hide file tree

Showing 4 changed files with 12 additions and 5 deletions.
diff --git a/docs/changelog.md b/docs/changelog.md
@@ -1,6 +1,11 @@
 # Change log
 All notable changes to this project will be documented in this file.
 
+## [0.9.1] -- 2020-07-13
+
+### Changed
+ - Fixed logic for no prealignments on first run
+
 ## [0.9.0] -- 2020-05-26
 
 ### Added

diff --git a/docs/usage.md b/docs/usage.md
@@ -21,7 +21,7 @@ usage: pepatac.py [-h] [-R] [-N] [-D] [-F] [-T] [--silent] [--verbosity V]
                   [--no-scale] [--prioritize] [--keep] [--noFIFO] [--lite]
                   [-V]
 
-PEPATAC version 0.9.0
+PEPATAC version 0.9.1
 
 optional arguments:
   -h, --help            show this help message and exit

diff --git a/pipelines/pepatac.py b/pipelines/pepatac.py
@@ -5,7 +5,7 @@
 
 __author__ = ["Jin Xu", "Nathan Sheffield", "Jason Smith"]
 __email__ = "[email protected]"
-__version__ = "0.9.0"
+__version__ = "0.9.1"
 
 
 from argparse import ArgumentParser
@@ -874,8 +874,10 @@ def main():
     os.chmod(tempdir, 0o771)
     pm.clean_add(tempdir)
 
-    unmap_fq1 = unmap_fq1 + ".gz"
-    unmap_fq2 = unmap_fq2 + ".gz"
+    # If there are no prealignments, unmap_fq1 will be unzipped
+    if pypiper.is_gzipped_fastq(unmap_fq1):
+        unmap_fq1 = unmap_fq1 + ".gz"
+        unmap_fq2 = unmap_fq2 + ".gz"
 
     bt2_index = os.path.join(rgc.seek(args.genome_assembly, BT2_IDX_KEY))
     if not bt2_index.endswith(args.genome_assembly):

diff --git a/usage.txt b/usage.txt
@@ -13,7 +13,7 @@ usage: pepatac.py [-h] [-R] [-N] [-D] [-F] [-T] [--silent] [--verbosity V]
                   [--no-scale] [--prioritize] [--keep] [--noFIFO] [--lite]
                   [-V]
 
-PEPATAC version 0.9.0
+PEPATAC version 0.9.1
 
 optional arguments:
   -h, --help            show this help message and exit