Merge pull request #696 from CGATOxford/{IS}_cram_support

{is} cram support

Author: IanSudbery

.github/workflows/tests.yml

@@ -32,5 +32,8 @@ jobs:
         run: |
           pip install .
       - name: Test with PyTest
+        env:
+          # This explicitly overrides the hardcoded RedHat paths inside the package
+          CURL_CA_BUNDLE: /etc/ssl/certs/ca-certificates.crt
         run: |
           pytest -v tests/test_umi_tools.py

tests/README

@@ -1,3 +1,7 @@
 Command to make test files for umi_tools extract --either-read testing:
 
 cd tests; paste <(zcat indrop.fastq.1.gz) <(zcat indrop.fastq.2.gz)|paste - - - - - - - -| awk -F "\t" 'BEGIN{OFS="\n"; srand(0)} {if(rand()>0.5) {print $1,$3,$5,$7 > "delete_me"; print $2,$4,$6,$8 > "delete_me2"} else {print $2,$4,$6,$8 > "delete_me"; print $1,$3,$5,$7 > "delete_me2"}}'; gzip delete_me2 -c > indrop.fastq.2_either_read.gz; gzip delete_me -c > indrop.fastq.1_either_read.gz; rm delete_me delete_me2
+
+
+Note that CRAM outputs are tested at the string decoded level using pysam, and not at the binary level. This avoids differences due to differenly installed compression libraries. 
+ 

tests/chr19_1mb.bam

@@ -68,6 +68,28 @@ Options:
     --per-cell          group/dedup/count per cell
 
   SAM/BAM options:
+    --in-format=IN_FORMAT
+                        File format of the input file. Format is usually
+                        implied from the extension of the filename, but maybe
+                        overridden with this option. Default=bam
+    --out-format=OUT_FORMAT
+                        File format of the input file. Format is usually
+                        implied from the extension of the filename, but maybe
+                        overridden with this option. Default=bam
+    --input-options=INPUT_OPTIONS
+                        Format string provided to htslib for reading. Mostly
+                        useful for CRAM formatted files. See samtools
+                        documentation
+    --output-options=OUTPUT_OPTIONS
+                        Format string provided to htslib for writing. Mostly
+                        useful for CRAM formatted files. See samtools
+                        documentation
+    --reference-filename=REFERENCE_FILENAME
+                        File path or URL to the genome reference to be used
+                        when reading or writing CRAM files. By default, when
+                        reading a CRAM file, the reference recorded in the
+                        input file will be used unless this is specified. When
+                        writing, specifying a reference location is required.
     --mapping-quality=MAPPING_QUALITY
                         Minimum mapping quality for a read to be retained
                         [default=0]

tests/chr19_1mb.bam.bai

@@ -78,6 +78,28 @@ Options:
                         the same position and umi [default=none]
 
   SAM/BAM options:
+    --in-format=IN_FORMAT
+                        File format of the input file. Format is usually
+                        implied from the extension of the filename, but maybe
+                        overridden with this option. Default=bam
+    --out-format=OUT_FORMAT
+                        File format of the input file. Format is usually
+                        implied from the extension of the filename, but maybe
+                        overridden with this option. Default=bam
+    --input-options=INPUT_OPTIONS
+                        Format string provided to htslib for reading. Mostly
+                        useful for CRAM formatted files. See samtools
+                        documentation
+    --output-options=OUTPUT_OPTIONS
+                        Format string provided to htslib for writing. Mostly
+                        useful for CRAM formatted files. See samtools
+                        documentation
+    --reference-filename=REFERENCE_FILENAME
+                        File path or URL to the genome reference to be used
+                        when reading or writing CRAM files. By default, when
+                        reading a CRAM file, the reference recorded in the
+                        input file will be used unless this is specified. When
+                        writing, specifying a reference location is required.
     --mapping-quality=MAPPING_QUALITY
                         Minimum mapping quality for a read to be retained
                         [default=0]