update readme

hasindu2008 · Jul 15, 2022 · 89e2b90 · 89e2b90
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diff --git a/README.md b/README.md
@@ -101,13 +101,25 @@ Follow the same steps as in [Nanopolish tutorial](https://nanopolish.readthedocs
 wget -O f5c_na12878_test.tgz "https://f5c.page.link/f5c_na12878_test"
 tar xf f5c_na12878_test.tgz
 
+###### Using FAST5 as input ######
+
 #index, call methylation and get methylation frequencies
 f5c index -d chr22_meth_example/fast5_files chr22_meth_example/reads.fastq
 f5c call-methylation -b chr22_meth_example/reads.sorted.bam -g chr22_meth_example/humangenome.fa -r chr22_meth_example/reads.fastq > chr22_meth_example/result.tsv
 f5c meth-freq -i chr22_meth_example/result.tsv > chr22_meth_example/freq.tsv
-
 #event alignment
 f5c eventalign -b chr22_meth_example/reads.sorted.bam -g chr22_meth_example/humangenome.fa -r chr22_meth_example/reads.fastq > chr22_meth_example/events.tsv
+
+###### Using SLOW5 as input ######
+
+#index, call methylation and get methylation frequencies
+f5c index --slow5 chr22_meth_example/reads.blow5 chr22_meth_example/reads.fastq
+f5c call-methylation --slow5 chr22_meth_example/reads.blow5 -b chr22_meth_example/reads.sorted.bam -g chr22_meth_example/humangenome.fa -r chr22_meth_example/reads.fastq > chr22_meth_example/result.tsv
+f5c meth-freq -i chr22_meth_example/result.tsv > chr22_meth_example/freq.tsv
+#event alignment
+f5c eventalign --slow5 chr22_meth_example/reads.blow5 -b chr22_meth_example/reads.sorted.bam -g chr22_meth_example/humangenome.fa -r chr22_meth_example/reads.fastq > chr22_meth_example/events.tsv
+
+
 ```
 
 ## Acknowledgement

diff --git a/src/index.c b/src/index.c
@@ -331,11 +331,12 @@ void parse_index_options(int argc, char** argv)
                 WARNING("%s","--iop is incompatible with sequencing summary files. Option --sequencing-summary-file will be ignored");
             }
         }
-        else {
-            if(opt::sequencing_summary_fofn.empty() && opt::sequencing_summary_files.empty()){
-                INFO("%s","Consider using --iop option for fast parallel indexing");
-            }
-        }
+        // else {
+        //     if(opt::sequencing_summary_fofn.empty() && opt::sequencing_summary_files.empty()){
+        //         INFO("%s","Consider using --iop option for fast parallel indexing");
+        //     }
+        // }
+        INFO("%s","Consider using --slow5 option for fast indexing, methylation calling and eventalignment. See f5c section under https://hasindu2008.github.io/slow5tools/workflows.html for an example.");
     } else{
         if(opt::iop > 1){
             WARNING("%s","Option --iop has no effect in slow5 mode");