update readme

Author: imsuneth

README.md

@@ -271,7 +271,7 @@ The output is ordered in the same as reads appear in the input BAM file. First c
 canonical_base(character such as ACGTN)|mod_code(character or ChEBI number)|status_flag(. or ?)
 ```
 
-Status flag describes how skipped bases (not included in the output of view or freq subtools) should be interpreted by downstream tools.
+Status flag describes how skipped bases should be interpreted by downstream tools.
 - **.** : skipped bases should be assumed to have low probability of modifications.
 - **?** : there is no information about the modification status of skipped bases
 
@@ -319,7 +319,29 @@ If the context is not specified in square brackets along with modification code,
 | N | n | Xao | Xanthosine | N |
 | N | N |  | Ambiguity code; any mod | N |
 
-Note that we have done a lot of testing on 5mc and some limited testing on 6mA and 5hmC. The others are not yet tested.
+## Supported and tested modifications
+
+Minimod is expected to support standard modifications given in the table above and any other either given as modification code or ChEBI code in MM tag of the BAM record.
+Note that we have done a lot of testing on 5mC and some limited testing on 6mA and 5hmC. The others are not thoroughly tested. Following is a summary of tests we have performed.
+
+| DNA/RNA | mod+base called model | aligned to | tested modification[context] combinations |
+| - | - | - | - |
+| DNA | 5mCG_5hmCG | hg38 genome | m[CG], h[CG], m[C], h[C], m[any], any[any] |
+| DNA | 4mC_5mC | hg38 genome | m[CG], m[C], 21839[C], any[any] |
+| DNA | 5mC_5hmC | hg38 genome | m[CG], h[CG], m[C], h[C], m[any], any[any] |
+| DNA | 6mA | hg38 genome | a[A], a[any], any[any] |
+| RNA | 2OmeG | hg38 genome | 19229[G], 19229[any], any[any] |
+| RNA | inosine_m6A_2OmeA | hg38 genome | 69426[A], a[A], 17596[A], any[any] |
+| RNA | m5C_2OmeC | hg38 genome | 19228[C], m[C], any[any] |
+| RNA | m6A_DRACH | hg38 genome | a[A], any[any] |
+| RNA | pseU_2OmeU | hg38 genome | 19227[T], 17802[T], any[any] |
+| RNA | m5C_2OmeC_inosine_m6A_2OmeA_pseU_2OmeU_2OmeG | hg38 genome | 17596[A], any[any] |
+| RNA | 2OmeG | gencode.v40 transcriptome | 19229[G], 19229[any] |
+| RNA | inosine_m6A_2OmeA | gencode.v40 transcriptome | 69426[A], a[A], 17596[A] |
+| RNA | m5C_2OmeC | gencode.v40 transcriptome | 19228[C], m[C], any[any] |
+| RNA | m6A_DRACH | gencode.v40 transcriptome | a[A], any[any] |
+| RNA | pseU_2OmeU | gencode.v40 transcriptome | 19227[T], 17802[T], any[any] |
+| RNA | m5C_2OmeC_inosine_m6A_2OmeA_pseU_2OmeU_2OmeG | gencode.v40 transcriptome | 69426[A], any[any] |
 
 # Modification threshold
 Base modification threshold can be set for freq tool using -m option.

test/test.sh

@@ -602,7 +602,7 @@ echo -e "${GREEN}${testname} passed!${NC}\n"
 
 
 
-#************** dna_5mCG_5hmCG_mm_chr22 C|h|. C|m|. **************
+#************** dna_5mC_5hmC_mm_chr22 C|h|. C|m|. **************
 testname="view m[CG] dna_5mC_5hmC_mm_chr22.bam"
 echo -e "${BLUE}${testname}${NC}"
 ex  ./minimod view --skip-supplementary -c m[CG] test/tmp/genome_chr22.fa test/data/dna_5mC_5hmC_mm_chr22.bam > test/tmp/dna_5mC_5hmC_mm_chr22.mm.view.m.CG.tsv || die "${testname} Running the tool failed"