ENCD-6111-add-compartments-output-type

src/encoded/schemas/analysis_step.json

@@ -121,6 +121,7 @@
                     "chromatin interactions",
                     "chromosomes reference",
                     "chromosome sizes",
+                    "compartments",
                     "consensus DNase hypersensitivity sites",
                     "conservative IDR thresholded peaks",
                     "control normalized signal",
@@ -311,6 +312,7 @@
                     "chromatin interactions",
                     "chromosomes reference",
                     "chromosome sizes",
+                    "compartments",
                     "consensus DNase hypersensitivity sites",
                     "conservative IDR thresholded peaks",
                     "control normalized signal",

src/encoded/schemas/changelogs/analysis_step.md

@@ -16,6 +16,7 @@
 * Added *genome compartment identification* to the enum list for *analysis_step_types*
 * Added *sparse peak count matrix* to the enum lists for *input_file_types* and *output_file_types*
 * Added *functional conservation quantifications* to the enum lists for *input_file_types* and *output_file_types*
+* Added *compartments* to the enum lists for *input_file_types* and *output_file_types*
 
 ### Schema version 15
 * *input_file_types*, *output_file_types* enums *blacklisted regions* and *mitochondria blacklisted regions* were replaced by *exclusion list regions* and *mitochondrial exclusion list regions* respectively 

src/encoded/schemas/changelogs/file.md

@@ -8,6 +8,7 @@
 * Added *fragments* to the enum list for *output_type*, the new output type is to be submitted as tar.gz only
 * Added *sparse peak count matrix* to the enum list for *output_type*
 * Added *functional conservation quantifications* to the enum list for *output_type*
+* Added *compartments* to the enum list for *output_type*
 
 ### Schema version 29
 * Added Ultima Genomics platform to dependency that enforces that *read_length* property should not be specified for FASTQ files produced by Oxford Nanopore and PacBio platforms.

src/encoded/schemas/file.json

@@ -1598,6 +1598,7 @@
                         "chromatin interactions",
                         "chromosomes reference",
                         "chromosome sizes",
+                        "compartments",
                         "consensus DNase hypersensitivity sites",
                         "curated binding sites",
                         "curated SNVs",
@@ -2359,6 +2360,7 @@
         "unidirectional peaks": "annotation",
         "polyA sites": "annotation",
         "functional conservation quantifications": "annotation",
+        "compartments": "annotation",
 
         "transcriptome reference": "reference",
         "transcriptome index": "reference",

src/encoded/tests/data/inserts/file.json

@@ -4745,5 +4745,22 @@
         "output_type": "functional conservation quantifications",
         "lab": "/labs/richard-myers/",
         "aliases": ["hongkai-ji:human_elements_scored_file"]
+    },
+    {
+        "_test": "Hi-C compartments",
+        "status": "in progress",
+        "submitted_file_name": "hi-c_compartments.bed.gz",
+        "uuid": "9ddfc5b8-2e9c-4ba2-a8b4-e5a0897a32cc",
+        "submitted_by": "[email protected]",
+        "md5sum": "9ddfc5b806a832272e691bd4e2bb622a",
+        "accession": "ENCFF333HIC",
+        "file_format": "bigWig",
+        "award": "/awards/U54HG006998/",
+        "assembly": "GRCh38",
+        "dataset": "/experiments/ENCSR000AJK/",
+        "file_size": 18000000,
+        "output_type": "compartments",
+        "lab": "/labs/richard-myers/",
+        "aliases": ["erez-aiden:hi-c_compartments"]
     }
 ]