Merge pull request #111 from broadinstitute/dp-libstats

isnv bug fixes
broadinstitute · Mar 11, 2015 · 5c38693 · 5c38693
2 parents 1c75f78 + dc6cb40
commit 5c38693
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Showing 19 changed files with 15 additions and 7,097 deletions.
diff --git a/data/snpEff/zebov.sl/genes.gbk b/data/snpEff/zebov.sl/genes.gbk
diff --git a/intrahost.py b/intrahost.py
@@ -144,7 +144,8 @@ def compute_library_bias(isnvs, inBam, inConsFasta) :
     '''
     alleleCol = 7 # First column of output with allele counts
     samtoolsTool = SamtoolsTool()
-    readGroups = samtoolsTool.getReadGroups(inBam)
+    readGroups = list(r for r in samtoolsTool.getReadGroups(inBam)
+        if samtoolsTool.count(inBam, ['-r', r])>0)
     tempDir = tempfile.mkdtemp()
     libBams = [os.path.join(tempDir, groupID + '.bam') for groupID in readGroups]
     for groupID, libBam in zip(readGroups, libBams) :
@@ -233,6 +234,9 @@ def get_mpileup_allele_counts(inBam, chrom, pos, inConsFasta) :
                             '-f', inConsFasta])
     with open(pileupFileName) as pileupFile :
         words = pileupFile.readline().split('\t')
+    if len(words)<5:
+        # empty output files means no reads pile up on this position
+        return {}
     alleleCounts = parse_alleles_string(words[4])
 
     # '.' is whatever mpileup thinks is the reference base (which might be

diff --git a/old-scripts/dpark/gene_stats.py b/old-scripts/dpark/gene_stats.py
diff --git a/old-scripts/iSNV/example_files/patients_all.txt b/old-scripts/iSNV/example_files/patients_all.txt
diff --git a/old-scripts/iSNV/example_files/vphaser_iSNVs_combined_NXT1.txt b/old-scripts/iSNV/example_files/vphaser_iSNVs_combined_NXT1.txt
diff --git a/old-scripts/iSNV/example_files/vphaser_iSNVs_combined_NXT1_freq.txt b/old-scripts/iSNV/example_files/vphaser_iSNVs_combined_NXT1_freq.txt
diff --git a/old-scripts/iSNV/example_files/vphaser_iSNVs_combined_NXT1_freq_validated.txt b/old-scripts/iSNV/example_files/vphaser_iSNVs_combined_NXT1_freq_validated.txt
diff --git a/old-scripts/iSNV/example_files/vphaser_iSNVs_combined_NXT2.txt b/old-scripts/iSNV/example_files/vphaser_iSNVs_combined_NXT2.txt
diff --git a/old-scripts/iSNV/iSNV-pipeline-edited.txt b/old-scripts/iSNV/iSNV-pipeline-edited.txt
diff --git a/old-scripts/iSNV/iSNV-pipeline.txt b/old-scripts/iSNV/iSNV-pipeline.txt