test hmmratac on frag file and barcodes file

Author: taoliu

test/cmdlinetest

@@ -1,5 +1,5 @@
 #!/bin/bash
-# Time-stamp: <2025-02-15 14:49:29 Tao Liu>
+# Time-stamp: <2025-10-17 11:39:29 Tao Liu>
 
 # integrative subcmds testing
 
@@ -243,10 +243,13 @@ echo "15.1 hmmratac load training regions from bedfile"
 macs3 hmmratac -i $ATACSEQBAM -n hmmratac_yeast500k_load_training_regions -t ${TRAINING_REGIONS_BED} --outdir ${OUTPUTDIR_PREFIX}_run_hmmratac &> ${OUTPUTDIR_PREFIX}_run_hmmratac/run_hmmratac_load_training_regions.log
 macs3 hmmratac -i $ATACSEQBAM --hmm-type poisson -n hmmratac_yeast500k_poisson_load_training_regions -t ${TRAINING_REGIONS_BED_POISSON} --outdir ${OUTPUTDIR_PREFIX}_run_hmmratac &> ${OUTPUTDIR_PREFIX}_run_hmmratac/run_hmmratac_load_training_regions_poisson.log
 
-# echo "15.2 hmmratac load hmm model file"
+echo "15.2 hmmratac load hmm model file"
 macs3 hmmratac -i $ATACSEQBAM -n hmmratac_yeast500k_load_hmm_model --model ${HMM_MODEL} --outdir ${OUTPUTDIR_PREFIX}_run_hmmratac &> ${OUTPUTDIR_PREFIX}_run_hmmratac/run_hmmratac_load_hmm_model.log
 macs3 hmmratac -i $ATACSEQBAM --hmm-type poisson -n hmmratac_yeast500k_poisson_load_hmm_model --model ${HMM_MODEL_POISSON} --outdir ${OUTPUTDIR_PREFIX}_run_hmmratac &> ${OUTPUTDIR_PREFIX}_run_hmmratac/run_hmmratac_load_hmm_model_poisson.log
 
+echo "15.3 hmmratac scATAC test"
+macs3 hmmratac -i $FRAGFILE -f FRAG --barcodes $BARCODESFILE -n hmmratac_scatac_test --hmm-type poisson -n hmmratac_scatac_test --outdir ${OUTPUTDIR_PREFIX}_run_hmmratac &> ${OUTPUTDIR_PREFIX}_run_hmmratac/run_hmmratac_scatac.log
+
 echo "16. search for errors in log files"
 flag=0
 for i in `ls ${OUTPUTDIR_PREFIX}_run_*/*.log`;do

test/yeast_500k_SRR1822137.barcode.txt

@@ -0,0 +1 @@
+BBBBBBBBBBBBBBBB