ex-282 (jebene/cgates) attempt to fix newline issue on travis

examples/README.rst

@@ -0,0 +1,31 @@
+=================
+Example VCF Files
+=================
+The vcfs directory contains example VCF files to be used as input for merge.
+These files have been de-identified and represent 5 patients.
+
+Usage
+=====
+
+To use Jacquard with the example data, run the following commands. Note that
+examples/vcfs is the input directory for translate.
+
+**translate**
+
+``$jacquard translate examples/00-input_vcfs <output_dir> [options]``
+
+**merge**
+
+``$jacquard merge examples/01-translated <output_vcf_file> [options]``
+
+**summarize**
+
+``$jacquard summarize examples/02-merged.vcf <output_vcf_file> [options]``
+
+**expand**
+
+``$jacquard expand exmaples/03-summarized.vcf <output_tsv_file> [options]``
+
+|
+|
+Refer to Jacquard/README.rst for more usage details

examples/examples_test.py

@@ -23,7 +23,7 @@ def test_examples(self):
                                         "00-input_vcfs")
             outputs = {"translate": "01-translated",
                        "merge": "02-merged.vcf",
-                       "summarize": "03-summarize.vcf",
+                       "summarize": "03-summarized.vcf",
                        "expand": "04-expanded.tsv"}
 
             translate_out = os.path.join(output_dir.path, outputs["translate"])

jacquard/utils/vcf.py

@@ -181,7 +181,7 @@ def parse_record(cls, vcf_line, sample_names):
         Returns:
             A mutable VcfRecord.
         """
-        vcf_fields = vcf_line.rstrip("\n").split("\t")
+        vcf_fields = vcf_line.rstrip("\r\n").split("\t")
         chrom, pos, rid, ref, alt, qual, rfilter, info \
                 = vcf_fields[0:8]
         sample_fields = []