BugFix

- Fixed problems with older versions of samtools which caused crashes
due to missing "supplementary reads" count in output.
- Fixed false warnings when parsing samtools flagstat output (has no
effect on final output)

Author: Dominik R Laetsch

bloblib/BtIO.py

@@ -186,19 +186,20 @@ def checkBam(infile):
     if not which('samtools'):
         BtLog.error('7')
     reads_mapped_re = re.compile(r"(\d+)\s\+\s\d+\smapped")
-    reads_secondary_re = re.compile(r"(\d+)\s\+\s\d+\ssecondary")
-    reads_supplementary_re = re.compile(r"(\d+)\s\+\s\d+\ssupplementary")
+    #reads_secondary_re = re.compile(r"(\d+)\s\+\s\d+\ssecondary")
+    #reads_supplementary_re = re.compile(r"(\d+)\s\+\s\d+\ssupplementary")
     reads_total_re = re.compile(r"(\d+)\s\+\s\d+\sin total")
     reads_total, reads_mapped = 0, 0
     output = ''
     command = "samtools flagstat " + infile
     for line in runCmd(command=command):
         output += line
     reads_mapped = int(reads_mapped_re.search(output).group(1))
-    reads_secondary = int(reads_secondary_re.search(output).group(1))
-    reads_supplementary = int(reads_supplementary_re.search(output).group(1))
-    reads_mapped = reads_mapped - reads_secondary - reads_supplementary
-    reads_total = int(reads_total_re.search(output).group(1)) - reads_secondary - reads_supplementary
+    #reads_secondary = int(reads_secondary_re.search(output).group(1))
+    #reads_supplementary = int(reads_supplementary_re.search(output).group(1))
+    #reads_mapped = reads_mapped - reads_secondary - reads_supplementary
+    reads_total = int(reads_total_re.search(output).group(1)) # - reads_secondary - reads_supplementary
+
     # check whether there are reads in BAM
     if not reads_total or not reads_mapped:
         BtLog.error('29' % infile)

test_files/blobDB.json

@@ -1 +1 @@
-{"nodesDB_f": "/Users/dominik/git/blobtools/data/nodesDB.txt", "lineages": {"6252": {"superkingdom": "Eukaryota", "family": "Ascarididae", "order": "Ascaridida", "phylum": "Nematoda", "genus": "Ascaris", "species": "Ascaris lumbricoides"}, "232323": {"superkingdom": "Eukaryota", "family": "Hypsibiidae", "order": "Parachela", "phylum": "Tardigrada", "genus": "Hypsibius", "species": "Hypsibius dujardini"}, "979556": {"superkingdom": "Bacteria", "family": "Microbacteriaceae", "order": "Micrococcales", "phylum": "Actinobacteria", "genus": "Microbacterium", "species": "Microbacterium testaceum"}}, "seqs": 10, "n_count": 0, "assembly_f": "/Users/dominik/git/blobtools/test_files/assembly.fna", "covLibs": {"bam0": {"reads_unmapped": 0, "mean_cov": 147.77711237724947, "cov_sum": 1477.7711237724945, "name": "bam0", "f": "/Users/dominik/git/blobtools/test_files/mapping_1.bam", "fmt": "bam", "reads_total": 15313, "reads_mapped": 15313}}, "title": "blobDB.json", "taxrules": ["bestsum"], "length": 18477, "version": "blobtools v0.9.19", "order_of_blobs": ["contig_1", "contig_2", "contig_3", "contig_4", "contig_5", "contig_6", "contig_7", "contig_8", "contig_9", "contig_10"], "hitLibs": {"tax1": {"fmt": "tax", "name": "tax1", "f": "/Users/dominik/git/blobtools/test_files/diamond.out"}, "tax0": {"fmt": "tax", "name": "tax0", "f": "/Users/dominik/git/blobtools/test_files/blast.out"}}, "dict_of_blobs": {"contig_10": {"hits": {}, "name": "contig_10", "taxonomy": {"bestsum": {"superkingdom": {"score": 0.0, "tax": "no-hit", "c_index": null}, "family": {"score": 0.0, "tax": "no-hit", "c_index": null}, "order": {"score": 0.0, "tax": "no-hit", "c_index": null}, "phylum": {"score": 0.0, "tax": "no-hit", "c_index": null}, "genus": {"score": 0.0, "tax": "no-hit", "c_index": null}, "species": {"score": 0.0, "tax": "no-hit", "c_index": null}}}, "agct_count": 6273, "length": 6273, "gc": 0.3067, "n_count": 0, "covs": {"bam0": 310.6336681013869}, "read_cov": {"bam0": 8741}}, "contig_9": {"hits": {"tax1": [{"score": 100.0, "name": "contig_9", "taxId": "6252"}], "tax0": [{"score": 200.0, "name": "contig_9", "taxId": "6252"}]}, "name": "contig_9", "taxonomy": {"bestsum": {"superkingdom": {"score": 300.0, "tax": "Eukaryota", "c_index": 0}, "family": {"score": 300.0, "tax": "Ascarididae", "c_index": 0}, "order": {"score": 300.0, "tax": "Ascaridida", "c_index": 0}, "phylum": {"score": 300.0, "tax": "Nematoda", "c_index": 0}, "genus": {"score": 300.0, "tax": "Ascaris", "c_index": 0}, "species": {"score": 300.0, "tax": "Ascaris lumbricoides", "c_index": 0}}}, "agct_count": 1599, "length": 1599, "gc": 0.2439, "n_count": 0, "covs": {"bam0": 74.7567229518449}, "read_cov": {"bam0": 554}}, "contig_8": {"hits": {"tax0": [{"score": 2000.0, "name": "contig_8", "taxId": "6252"}, {"score": 2000.0, "name": "contig_8", "taxId": "979556"}]}, "name": "contig_8", "taxonomy": {"bestsum": {"superkingdom": {"score": 2000.0, "tax": "unresolved", "c_index": 1}, "family": {"score": 2000.0, "tax": "unresolved", "c_index": 1}, "order": {"score": 2000.0, "tax": "unresolved", "c_index": 1}, "phylum": {"score": 2000.0, "tax": "unresolved", "c_index": 1}, "genus": {"score": 2000.0, "tax": "unresolved", "c_index": 1}, "species": {"score": 2000.0, "tax": "unresolved", "c_index": 1}}}, "agct_count": 2346, "length": 2346, "gc": 0.2801, "n_count": 0, "covs": {"bam0": 91.74211423699914}, "read_cov": {"bam0": 1008}}, "contig_1": {"hits": {"tax1": [{"score": 200.0, "name": "contig_1", "taxId": "232323"}], "tax0": [{"score": 200.0, "name": "contig_1", "taxId": "979556"}]}, "name": "contig_1", "taxonomy": {"bestsum": {"superkingdom": {"score": 200.0, "tax": "unresolved", "c_index": 1}, "family": {"score": 200.0, "tax": "unresolved", "c_index": 1}, "order": {"score": 200.0, "tax": "unresolved", "c_index": 1}, "phylum": {"score": 200.0, "tax": "unresolved", "c_index": 1}, "genus": {"score": 200.0, "tax": "unresolved", "c_index": 1}, "species": {"score": 200.0, "tax": "unresolved", "c_index": 1}}}, "agct_count": 756, "length": 756, "gc": 0.2606, "n_count": 0, "covs": {"bam0": 90.40608465608466}, "read_cov": {"bam0": 369}}, "contig_3": {"hits": {"tax1": [{"score": 10000.0, "name": "contig_3", "taxId": "979556"}], "tax0": [{"score": 10000.0, "name": "contig_3", "taxId": "979556"}]}, "name": "contig_3", "taxonomy": {"bestsum": {"superkingdom": {"score": 20000.0, "tax": "Bacteria", "c_index": 0}, "family": {"score": 20000.0, "tax": "Microbacteriaceae", "c_index": 0}, "order": {"score": 20000.0, "tax": "Micrococcales", "c_index": 0}, "phylum": {"score": 20000.0, "tax": "Actinobacteria", "c_index": 0}, "genus": {"score": 20000.0, "tax": "Microbacterium", "c_index": 0}, "species": {"score": 20000.0, "tax": "Microbacterium testaceum", "c_index": 0}}}, "agct_count": 602, "length": 602, "gc": 0.2342, "n_count": 0, "covs": {"bam0": 43.76079734219269}, "read_cov": {"bam0": 188}}, "contig_2": {"hits": {"tax1": [{"score": 500.0, "name": "contig_2", "taxId": "232323"}, {"score": 1000.0, "name": "contig_2", "taxId": "232323"}, {"score": 500.0, "name": "contig_2", "taxId": "232323"}, {"score": 300.0, "name": "contig_2", "taxId": "979556"}], "tax0": [{"score": 500.0, "name": "contig_2", "taxId": "979556"}, {"score": 1000.0, "name": "contig_2", "taxId": "979556"}, {"score": 500.0, "name": "contig_2", "taxId": "979556"}, {"score": 300.0, "name": "contig_2", "taxId": "979556"}]}, "name": "contig_2", "taxonomy": {"bestsum": {"superkingdom": {"score": 2600.0, "tax": "Bacteria", "c_index": 1}, "family": {"score": 2600.0, "tax": "Microbacteriaceae", "c_index": 1}, "order": {"score": 2600.0, "tax": "Micrococcales", "c_index": 1}, "phylum": {"score": 2600.0, "tax": "Actinobacteria", "c_index": 1}, "genus": {"score": 2600.0, "tax": "Microbacterium", "c_index": 1}, "species": {"score": 2600.0, "tax": "Microbacterium testaceum", "c_index": 1}}}, "agct_count": 1060, "length": 1060, "gc": 0.2623, "n_count": 0, "covs": {"bam0": 168.40943396226416}, "read_cov": {"bam0": 844}}, "contig_5": {"hits": {"tax1": [{"score": 1000.0, "name": "contig_5", "taxId": "6252"}], "tax0": [{"score": 2000.0, "name": "contig_5", "taxId": "6252"}]}, "name": "contig_5", "taxonomy": {"bestsum": {"superkingdom": {"score": 3000.0, "tax": "Eukaryota", "c_index": 0}, "family": {"score": 3000.0, "tax": "Ascarididae", "c_index": 0}, "order": {"score": 3000.0, "tax": "Ascaridida", "c_index": 0}, "phylum": {"score": 3000.0, "tax": "Nematoda", "c_index": 0}, "genus": {"score": 3000.0, "tax": "Ascaris", "c_index": 0}, "species": {"score": 3000.0, "tax": "Ascaris lumbricoides", "c_index": 0}}}, "agct_count": 614, "length": 614, "gc": 0.329, "n_count": 0, "covs": {"bam0": 163.557003257329}, "read_cov": {"bam0": 456}}, "contig_4": {"hits": {"tax1": [{"score": 1000.0, "name": "contig_4", "taxId": "979556"}], "tax0": [{"score": 1000.0, "name": "contig_4", "taxId": "979556"}]}, "name": "contig_4", "taxonomy": {"bestsum": {"superkingdom": {"score": 2000.0, "tax": "Bacteria", "c_index": 0}, "family": {"score": 2000.0, "tax": "Microbacteriaceae", "c_index": 0}, "order": {"score": 2000.0, "tax": "Micrococcales", "c_index": 0}, "phylum": {"score": 2000.0, "tax": "Actinobacteria", "c_index": 0}, "genus": {"score": 2000.0, "tax": "Microbacterium", "c_index": 0}, "species": {"score": 2000.0, "tax": "Microbacterium testaceum", "c_index": 0}}}, "agct_count": 951, "length": 951, "gc": 0.3155, "n_count": 0, "covs": {"bam0": 456.31335436382756}, "read_cov": {"bam0": 2096}}, "contig_7": {"hits": {"tax1": [{"score": 1000.0, "name": "contig_7", "taxId": "6252"}], "tax0": [{"score": 2000.0, "name": "contig_7", "taxId": "6252"}]}, "name": "contig_7", "taxonomy": {"bestsum": {"superkingdom": {"score": 3000.0, "tax": "Eukaryota", "c_index": 0}, "family": {"score": 3000.0, "tax": "Ascarididae", "c_index": 0}, "order": {"score": 3000.0, "tax": "Ascaridida", "c_index": 0}, "phylum": {"score": 3000.0, "tax": "Nematoda", "c_index": 0}, "genus": {"score": 3000.0, "tax": "Ascaris", "c_index": 0}, "species": {"score": 3000.0, "tax": "Ascaris lumbricoides", "c_index": 0}}}, "agct_count": 4060, "length": 4060, "gc": 0.2584, "n_count": 0, "covs": {"bam0": 52.31231527093596}, "read_cov": {"bam0": 1005}}, "contig_6": {"hits": {"tax1": [{"score": 1000.0, "name": "contig_6", "taxId": "232323"}, {"score": 1000.0, "name": "contig_6", "taxId": "6252"}, {"score": 1000.0, "name": "contig_6", "taxId": "979556"}, {"score": 1000.0, "name": "contig_6", "taxId": "232323"}], "tax0": [{"score": 2000.0, "name": "contig_6", "taxId": "232323"}, {"score": 2000.0, "name": "contig_6", "taxId": "6252"}, {"score": 2000.0, "name": "contig_6", "taxId": "979556"}, {"score": 2000.0, "name": "contig_6", "taxId": "232323"}]}, "name": "contig_6", "taxonomy": {"bestsum": {"superkingdom": {"score": 9000.0, "tax": "Eukaryota", "c_index": 1}, "family": {"score": 6000.0, "tax": "Hypsibiidae", "c_index": 2}, "order": {"score": 6000.0, "tax": "Parachela", "c_index": 2}, "phylum": {"score": 6000.0, "tax": "Tardigrada", "c_index": 2}, "genus": {"score": 6000.0, "tax": "Hypsibius", "c_index": 2}, "species": {"score": 6000.0, "tax": "Hypsibius dujardini", "c_index": 2}}}, "agct_count": 216, "length": 216, "gc": 0.1944, "n_count": 0, "covs": {"bam0": 25.87962962962963}, "read_cov": {"bam0": 52}}}}
+{"nodesDB_f": "/Users/dom/git/blobtools/data/nodesDB.txt", "lineages": {"6252": {"superkingdom": "Eukaryota", "family": "Ascarididae", "order": "Ascaridida", "phylum": "Nematoda", "genus": "Ascaris", "species": "Ascaris lumbricoides"}, "232323": {"superkingdom": "Eukaryota", "family": "Hypsibiidae", "order": "Parachela", "phylum": "Tardigrada", "genus": "Hypsibius", "species": "Hypsibius dujardini"}, "979556": {"superkingdom": "Bacteria", "family": "Microbacteriaceae", "order": "Micrococcales", "phylum": "Actinobacteria", "genus": "Microbacterium", "species": "Microbacterium testaceum"}}, "seqs": 10, "n_count": 0, "assembly_f": "/Users/dom/git/blobtools/test_files/assembly.fna", "covLibs": {"bam0": {"reads_unmapped": 0, "mean_cov": 147.77711237724947, "cov_sum": 1477.7711237724945, "name": "bam0", "f": "/Users/dom/git/blobtools/test_files/mapping_1.bam", "fmt": "bam", "reads_total": 15313, "reads_mapped": 15313}}, "title": "test_files/blobDB.json", "taxrules": ["bestsum"], "length": 18477, "version": "blobtools v0.9.19", "order_of_blobs": ["contig_1", "contig_2", "contig_3", "contig_4", "contig_5", "contig_6", "contig_7", "contig_8", "contig_9", "contig_10"], "hitLibs": {"tax0": {"fmt": "tax", "name": "tax0", "f": "/Users/dom/git/blobtools/test_files/blast.out"}}, "dict_of_blobs": {"contig_10": {"hits": {}, "name": "contig_10", "taxonomy": {"bestsum": {"superkingdom": {"score": 0.0, "tax": "no-hit", "c_index": null}, "family": {"score": 0.0, "tax": "no-hit", "c_index": null}, "order": {"score": 0.0, "tax": "no-hit", "c_index": null}, "phylum": {"score": 0.0, "tax": "no-hit", "c_index": null}, "genus": {"score": 0.0, "tax": "no-hit", "c_index": null}, "species": {"score": 0.0, "tax": "no-hit", "c_index": null}}}, "agct_count": 6273, "length": 6273, "gc": 0.3067, "n_count": 0, "covs": {"bam0": 310.634}, "read_cov": {"bam0": 8741}}, "contig_9": {"hits": {"tax0": [{"score": 200.0, "name": "contig_9", "taxId": "6252"}]}, "name": "contig_9", "taxonomy": {"bestsum": {"superkingdom": {"score": 200.0, "tax": "Eukaryota", "c_index": 0}, "family": {"score": 200.0, "tax": "Ascarididae", "c_index": 0}, "order": {"score": 200.0, "tax": "Ascaridida", "c_index": 0}, "phylum": {"score": 200.0, "tax": "Nematoda", "c_index": 0}, "genus": {"score": 200.0, "tax": "Ascaris", "c_index": 0}, "species": {"score": 200.0, "tax": "Ascaris lumbricoides", "c_index": 0}}}, "agct_count": 1599, "length": 1599, "gc": 0.2439, "n_count": 0, "covs": {"bam0": 74.757}, "read_cov": {"bam0": 554}}, "contig_8": {"hits": {"tax0": [{"score": 2000.0, "name": "contig_8", "taxId": "6252"}, {"score": 2000.0, "name": "contig_8", "taxId": "979556"}]}, "name": "contig_8", "taxonomy": {"bestsum": {"superkingdom": {"score": 2000.0, "tax": "unresolved", "c_index": 1}, "family": {"score": 2000.0, "tax": "unresolved", "c_index": 1}, "order": {"score": 2000.0, "tax": "unresolved", "c_index": 1}, "phylum": {"score": 2000.0, "tax": "unresolved", "c_index": 1}, "genus": {"score": 2000.0, "tax": "unresolved", "c_index": 1}, "species": {"score": 2000.0, "tax": "unresolved", "c_index": 1}}}, "agct_count": 2346, "length": 2346, "gc": 0.2801, "n_count": 0, "covs": {"bam0": 91.742}, "read_cov": {"bam0": 1008}}, "contig_1": {"hits": {"tax0": [{"score": 200.0, "name": "contig_1", "taxId": "979556"}]}, "name": "contig_1", "taxonomy": {"bestsum": {"superkingdom": {"score": 200.0, "tax": "Bacteria", "c_index": 0}, "family": {"score": 200.0, "tax": "Microbacteriaceae", "c_index": 0}, "order": {"score": 200.0, "tax": "Micrococcales", "c_index": 0}, "phylum": {"score": 200.0, "tax": "Actinobacteria", "c_index": 0}, "genus": {"score": 200.0, "tax": "Microbacterium", "c_index": 0}, "species": {"score": 200.0, "tax": "Microbacterium testaceum", "c_index": 0}}}, "agct_count": 756, "length": 756, "gc": 0.2606, "n_count": 0, "covs": {"bam0": 90.406}, "read_cov": {"bam0": 369}}, "contig_3": {"hits": {"tax0": [{"score": 10000.0, "name": "contig_3", "taxId": "979556"}]}, "name": "contig_3", "taxonomy": {"bestsum": {"superkingdom": {"score": 10000.0, "tax": "Bacteria", "c_index": 0}, "family": {"score": 10000.0, "tax": "Microbacteriaceae", "c_index": 0}, "order": {"score": 10000.0, "tax": "Micrococcales", "c_index": 0}, "phylum": {"score": 10000.0, "tax": "Actinobacteria", "c_index": 0}, "genus": {"score": 10000.0, "tax": "Microbacterium", "c_index": 0}, "species": {"score": 10000.0, "tax": "Microbacterium testaceum", "c_index": 0}}}, "agct_count": 602, "length": 602, "gc": 0.2342, "n_count": 0, "covs": {"bam0": 43.761}, "read_cov": {"bam0": 188}}, "contig_2": {"hits": {"tax0": [{"score": 500.0, "name": "contig_2", "taxId": "979556"}, {"score": 1000.0, "name": "contig_2", "taxId": "979556"}, {"score": 500.0, "name": "contig_2", "taxId": "979556"}, {"score": 300.0, "name": "contig_2", "taxId": "979556"}]}, "name": "contig_2", "taxonomy": {"bestsum": {"superkingdom": {"score": 2300.0, "tax": "Bacteria", "c_index": 0}, "family": {"score": 2300.0, "tax": "Microbacteriaceae", "c_index": 0}, "order": {"score": 2300.0, "tax": "Micrococcales", "c_index": 0}, "phylum": {"score": 2300.0, "tax": "Actinobacteria", "c_index": 0}, "genus": {"score": 2300.0, "tax": "Microbacterium", "c_index": 0}, "species": {"score": 2300.0, "tax": "Microbacterium testaceum", "c_index": 0}}}, "agct_count": 1060, "length": 1060, "gc": 0.2623, "n_count": 0, "covs": {"bam0": 168.409}, "read_cov": {"bam0": 844}}, "contig_5": {"hits": {"tax0": [{"score": 2000.0, "name": "contig_5", "taxId": "6252"}]}, "name": "contig_5", "taxonomy": {"bestsum": {"superkingdom": {"score": 2000.0, "tax": "Eukaryota", "c_index": 0}, "family": {"score": 2000.0, "tax": "Ascarididae", "c_index": 0}, "order": {"score": 2000.0, "tax": "Ascaridida", "c_index": 0}, "phylum": {"score": 2000.0, "tax": "Nematoda", "c_index": 0}, "genus": {"score": 2000.0, "tax": "Ascaris", "c_index": 0}, "species": {"score": 2000.0, "tax": "Ascaris lumbricoides", "c_index": 0}}}, "agct_count": 614, "length": 614, "gc": 0.329, "n_count": 0, "covs": {"bam0": 163.557}, "read_cov": {"bam0": 456}}, "contig_4": {"hits": {"tax0": [{"score": 1000.0, "name": "contig_4", "taxId": "979556"}]}, "name": "contig_4", "taxonomy": {"bestsum": {"superkingdom": {"score": 1000.0, "tax": "Bacteria", "c_index": 0}, "family": {"score": 1000.0, "tax": "Microbacteriaceae", "c_index": 0}, "order": {"score": 1000.0, "tax": "Micrococcales", "c_index": 0}, "phylum": {"score": 1000.0, "tax": "Actinobacteria", "c_index": 0}, "genus": {"score": 1000.0, "tax": "Microbacterium", "c_index": 0}, "species": {"score": 1000.0, "tax": "Microbacterium testaceum", "c_index": 0}}}, "agct_count": 951, "length": 951, "gc": 0.3155, "n_count": 0, "covs": {"bam0": 456.313}, "read_cov": {"bam0": 2096}}, "contig_7": {"hits": {"tax0": [{"score": 2000.0, "name": "contig_7", "taxId": "6252"}]}, "name": "contig_7", "taxonomy": {"bestsum": {"superkingdom": {"score": 2000.0, "tax": "Eukaryota", "c_index": 0}, "family": {"score": 2000.0, "tax": "Ascarididae", "c_index": 0}, "order": {"score": 2000.0, "tax": "Ascaridida", "c_index": 0}, "phylum": {"score": 2000.0, "tax": "Nematoda", "c_index": 0}, "genus": {"score": 2000.0, "tax": "Ascaris", "c_index": 0}, "species": {"score": 2000.0, "tax": "Ascaris lumbricoides", "c_index": 0}}}, "agct_count": 4060, "length": 4060, "gc": 0.2584, "n_count": 0, "covs": {"bam0": 52.312}, "read_cov": {"bam0": 1005}}, "contig_6": {"hits": {"tax0": [{"score": 2000.0, "name": "contig_6", "taxId": "232323"}, {"score": 2000.0, "name": "contig_6", "taxId": "6252"}, {"score": 2000.0, "name": "contig_6", "taxId": "979556"}, {"score": 2000.0, "name": "contig_6", "taxId": "232323"}]}, "name": "contig_6", "taxonomy": {"bestsum": {"superkingdom": {"score": 6000.0, "tax": "Eukaryota", "c_index": 1}, "family": {"score": 4000.0, "tax": "Hypsibiidae", "c_index": 2}, "order": {"score": 4000.0, "tax": "Parachela", "c_index": 2}, "phylum": {"score": 4000.0, "tax": "Tardigrada", "c_index": 2}, "genus": {"score": 4000.0, "tax": "Hypsibius", "c_index": 2}, "species": {"score": 4000.0, "tax": "Hypsibius dujardini", "c_index": 2}}}, "agct_count": 216, "length": 216, "gc": 0.1944, "n_count": 0, "covs": {"bam0": 25.88}, "read_cov": {"bam0": 52}}}}

test_files/mapping_1.bam.cov

@@ -2,15 +2,15 @@
 ## Total Reads = 15313
 ## Mapped Reads = 15313
 ## Unmapped Reads = 0
-## Source(s) : /Users/dominik/git/blobtools/test_files/mapping_1.bam
+## Source(s) : /Users/dom/git/blobtools/test_files/mapping_1.bam
 # contig_id	read_cov	base_cov
-contig_1	369	90.4060846561
-contig_2	844	168.409433962
-contig_3	188	43.7607973422
-contig_4	2096	456.313354364
-contig_5	456	163.557003257
-contig_6	52	25.8796296296
-contig_7	1005	52.3123152709
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