update readme

README.md

@@ -26,11 +26,11 @@ Clair3 is the 3<sup>rd</sup> generation of [Clair](https://github.com/HKU-BAL/Cl
 
 We are actively fixing bugs and issues in Clair3 reported by users.
 
-*v0.1-r5 (July 19)* : 1. Modified data generator in model training to avoid memory exhaustion and unexpected segmentation fault by Tensorflow (contributor @[ftostevin-ont](https://github.com/ftostevin-ont) ). 2. Simplified dockerfile workflow to reuse container caching (contributor @[amblina](https://github.com/amblina)**). 3. Fixed ALT output for reference calls (contributor @[wdecoster](https://github.com/wdecoster)). 4. Fixed a bug in multi-allelic AF computation (AF of [ACGT]Del variants was wrong before r5). 5. Added AD tag to the GVCF output. 6. Added the `--call_snp_only` option to only call SNP only ([#40](https://github.com/HKU-BAL/Clair3/issues/40)). 7. Added pileup and full-alignment output validity check to avoid workflow crashing ([#32](https://github.com/HKU-BAL/Clair3/issues/32), [#38](https://github.com/HKU-BAL/Clair3/issues/38)).
+*v0.1-r5 (July 19)* : 1. Modified data generator in model training to avoid memory exhaustion and unexpected segmentation fault by Tensorflow (contributor @[ftostevin-ont](https://github.com/ftostevin-ont) ). 2. Simplified dockerfile workflow to reuse container caching (contributor @[amblina](https://github.com/amblina)). 3. Fixed ALT output for reference calls (contributor @[wdecoster](https://github.com/wdecoster)). 4. Fixed a bug in multi-allelic AF computation (AF of [ACGT]Del variants was wrong before r5). 5. Added AD tag to the GVCF output. 6. Added the `--call_snp_only` option to only call SNP only ([#40](https://github.com/HKU-BAL/Clair3/issues/40)). 7. Added pileup and full-alignment output validity check to avoid workflow crashing ([#32](https://github.com/HKU-BAL/Clair3/issues/32), [#38](https://github.com/HKU-BAL/Clair3/issues/38)).
 
-*v0.1-r4 (Jun 28)* : 1. Install via [bioconda](https://github.com/HKU-BAL/Clair3#option-3--bioconda). 2. Added an ONT Guppy2 model to the images (`ont_guppy2`). Click [here](https://github.com/HKU-BAL/Clair3/blob/main/docs/guppy2.md) for more benchmarking results. **The results show you have to use the Guppy2 model for Guppy2 or earlier data**. 3. Added [google colab notebooks](https://github.com/HKU-BAL/Clair3/blob/main/colab) for quick demo. 4. Fixed a bug when there are too few variant candidates ([#28](https://github.com/HKU-BAL/Clair3/issues/28)).
+*v0.1-r4 (June 28)* : 1. Install via [bioconda](https://github.com/HKU-BAL/Clair3#option-3--bioconda). 2. Added an ONT Guppy2 model to the images (`ont_guppy2`). Click [here](https://github.com/HKU-BAL/Clair3/blob/main/docs/guppy2.md) for more benchmarking results. **The results show you have to use the Guppy2 model for Guppy2 or earlier data**. 3. Added [google colab notebooks](https://github.com/HKU-BAL/Clair3/blob/main/colab) for quick demo. 4. Fixed a bug when there are too few variant candidates ([#28](https://github.com/HKU-BAL/Clair3/issues/28)).
 
-*v0.1-r3 (Jun 9)* : 1. Added `ulimit -u` (max user processes) check (lowers the `THREADS` if the resource is insufficient) and automatic retries on failed jobs ([#20](https://github.com/HKU-BAL/Clair3/issues/20), [#23](https://github.com/HKU-BAL/Clair3/issues/23), [#24](https://github.com/HKU-BAL/Clair3/issues/24)). 2. Added an ONT Guppy5 model to the images (`ont_guppy5`). Click [here](docs/guppy5.md) for more benchmarks on the Guppy5 model and data.
+*v0.1-r3 (June 9)* : 1. Added `ulimit -u` (max user processes) check (lowers the `THREADS` if the resource is insufficient) and automatic retries on failed jobs ([#20](https://github.com/HKU-BAL/Clair3/issues/20), [#23](https://github.com/HKU-BAL/Clair3/issues/23), [#24](https://github.com/HKU-BAL/Clair3/issues/24)). 2. Added an ONT Guppy5 model to the images (`ont_guppy5`). Click [here](docs/guppy5.md) for more benchmarks on the Guppy5 model and data.
 
 *v0.1-r2 (May 23)* : 1. Fixed BED file out of range error ([#12](https://github.com/HKU-BAL/Clair3/issues/12)). 2. Added support for both `.bam.bai` and `.bai` BAM index filename ([#10](https://github.com/HKU-BAL/Clair3/issues/10)). 3. Added some boundary checks on inputs. 4. Added version checks on required packages and utilities. 5. Increased pipeline robusity.