Merge pull request #58 from HKU-BAL/fix_typo_of_ont_pr

Fix typo of ont pr
HKU-BAL · Sep 29, 2021 · 70ee1e7 · 70ee1e7
2 parents bb82e5f + 457c59d
commit 70ee1e7
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Showing 3 changed files with 4 additions and 7 deletions.
diff --git a/docs/full_alignment_training.md b/docs/full_alignment_training.md
@@ -283,7 +283,7 @@ ${PARALLEL} --joblog ${DATASET_FOLDER_PATH}/create_tensor_full_alignment.log -j$
 "${PYPY} ${CLAIR3} CreateTrainingTensor \
     --bam_fn {4} \
     --ref_fn {5} \
-    --var_fn ${VAR_OUTPUT_PATH}/var_{2}_{3}_{1}" \
+    --var_fn ${VAR_OUTPUT_PATH}/var_{2}_{3}_{1} \
     --bin_fn ${TENSOR_CANDIDATE_PATH}/tensor_{2}_{3}_{1}_{7} \
     --ctgName ${CHR_PREFIX}{1} \
     --samtools ${SAMTOOLS} \
@@ -316,8 +316,7 @@ ${PARALLEL} --joblog ${DATASET_FOLDER_PATH}/create_tensor_full_alignment.log -j$
 ${PARALLEL} --joblog ${DATASET_FOLDER_PATH}/mergeBin.log -j${THREADS} \
 "${PYTHON3} ${CLAIR3} MergeBin \
     ${TENSOR_CANDIDATE_PATH}/tensor_{2}_{3}_{1}_* \
-    --out_fn ${BINS_FOLDER_PATH}/bin_{2}_{3}_{1} \
-    --chunk_num ${bin_chunk_num}" ::: ${CHR[@]} ::: ${ALL_SAMPLE[@]} :::+ ${DEPTHS[@]}
+    --out_fn ${BINS_FOLDER_PATH}/bin_{2}_{3}_{1}" ::: ${CHR[@]} ::: ${ALL_SAMPLE[@]} :::+ ${DEPTHS[@]}
 
 ```
 

diff --git a/docs/pileup_training.md b/docs/pileup_training.md
@@ -230,7 +230,7 @@ ${PARALLEL} --joblog ${DATASET_FOLDER_PATH}/create_tensor_pileup.log -j${THREADS
 "${PYPY} ${CLAIR3} CreateTrainingTensor \
     --bam_fn {4} \
     --ref_fn {5} \
-    --var_fn ${VAR_OUTPUT_PATH}/var_{2}_{3}_{1}" \
+    --var_fn ${VAR_OUTPUT_PATH}/var_{2}_{3}_{1} \
     --bin_fn ${TENSOR_CANDIDATE_PATH}/tensor_{2}_{3}_{1}_{7} \
     --ctgName ${CHR_PREFIX}{1} \
     --samtools ${SAMTOOLS} \
@@ -262,8 +262,7 @@ ${PARALLEL} --joblog ${DATASET_FOLDER_PATH}/mergeBin.log -j${THREADS} \
 "${PYTHON3} ${CLAIR3} MergeBin \
     ${TENSOR_CANDIDATE_PATH}/tensor_{2}_{3}_{1}_* \
     --out_fn ${BINS_FOLDER_PATH}/bin_{2}_{3}_{1} \
-    --pileup \
-    --chunk_num ${bin_chunk_num}" ::: ${CHR[@]} ::: ${ALL_SAMPLE[@]} :::+ ${DEPTHS[@]}
+    --pileup" ::: ${CHR[@]} ::: ${ALL_SAMPLE[@]} :::+ ${DEPTHS[@]}
 
 ```
 

diff --git a/docs/representation_unification.md b/docs/representation_unification.md
@@ -162,7 +162,6 @@ ${PARALLEL} --joblog ${OUTPUT_DIR}/unify_repre.log -j${THREADS} \
     --bed_fn ${BED_FILE_PATH} \
     --extend_bed ${SPLIT_BED_PATH}/{1} \
     --output_vcf_fn ${VCF_OUTPUT_PATH}/vcf_{1}_{2} \
-    --samtools ${SAMTOOLS} \
     --min_af ${MIN_AF} \
     --chunk_id {2} \
     --chunk_num ${chunk_num} \