no read in bam error handling

nf-core · Oct 24, 2018 · aa53aa0 · aa53aa0
1 parent 7124bde
commit aa53aa0
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Showing 2 changed files with 11 additions and 7 deletions.
diff --git a/bin/normalizedReadCount b/bin/normalizedReadCount
@@ -184,11 +184,15 @@ def getNumberMappedReadsMultiprocess(bam, processes, id, commonReads=[]):
 
 
 def writeBam(inbam, outbam, commonReads):
-    bamin = pysam.AlignmentFile(inbam, "rb")
-    bamout = pysam.AlignmentFile(outbam, 'w', template=bamin)
-    for s in bamin:
-        if s.query_name not in commonReads:
-            bamout.write(s)
+    try:
+        bamin = pysam.AlignmentFile(inbam, "rb")
+        bamout = pysam.AlignmentFile(outbam, 'w', template=bamin)
+        for s in bamin:
+            if s.query_name not in commonReads:
+                bamout.write(s)
+    except ValueError:
+        with open("error_readme_"+outbam, "w") as o:
+            o.write("Error writing this BAM file, input bam file was erroneous")
 
 
 def getCommonReads(readsBam1, readsBam2):

diff --git a/bin/plotAndReport b/bin/plotAndReport
@@ -212,7 +212,7 @@ if __name__ == "__main__":
             fw.write(conclusion + '\n\n')
             fw.write("- **MapDamage plots**\n\n")
             fw.write("![MapDamage Fragmisincorporation plot for " +
-                     orga1_clean + ". Very jagged and irregular substitutions are likely indicating spurious damages caused by a lack of reads.](./" + asample + "." + d[asample]["orga1"] + ".fragmisincorporation_plot.png)\n\n")
+                     orga1_clean + ". Very jagged and irregular substitutions are likely indicating spurious damages caused by a lack of reads. If there is not plot displayed, the aligned read count was too low for mapDamage](./" + asample + "." + d[asample]["orga1"] + ".fragmisincorporation_plot.png)\n\n")
             fw.write("![MapDamage Fragmisincorporation plot for " +
-                     orga2_clean + ". Very jagged and irregular substitutions are likely indicating spurious damages caused by a lack of reads.](./" + asample + "." + d[asample]["orga2"] + ".fragmisincorporation_plot.png)\n\n")
+                     orga2_clean + ". Very jagged and irregular substitutions are likely indicating spurious damages caused by a lack of reads. If there is not plot displayed, the aligned read count was too low for mapDamage](./" + asample + "." + d[asample]["orga2"] + ".fragmisincorporation_plot.png)\n\n")
             fw.write("\n\n***\n")