Merge pull request #143 in SAT/pbmm2 from bugfix/TAK-994-portable-grep to develop

derekwbarnett · derekwbarnett · commit 89ac9117a17c · 2020-09-21T08:53:26.000-07:00
* commit '3e30a533cf567badd85c1113025bf412fa68d6c8':
  Restore portable grep in CRAM tests
diff --git a/tests/cram/splitsample.t b/tests/cram/splitsample.t
@@ -7,22 +7,22 @@
   $ ls -l $CRAMTMP/split.*.bam | wc -l | tr -d ' '
   3
 
-  $ ID=$(samtools view -F 4 -H $CRAMTMP/split.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam | grep 3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494 | grep -vP "@PG\tID:samtools" | cut -f 2 | cut -f 2 -d ':')
-  $ samtools view -F 4 $CRAMTMP/split.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam | grep -vc ${ID} | grep -vP "@PG\tID:samtools" | tr -d ' '
+  $ ID=$(samtools view -F 4 -H $CRAMTMP/split.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam | grep 3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494 | grep -v "@PG	ID:samtools" | cut -f 2 | cut -f 2 -d ':')
+  $ samtools view -F 4 $CRAMTMP/split.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam | grep -vc ${ID} | grep -v "@PG	ID:samtools" | tr -d ' '
   0
-  $ samtools view -F 4 $CRAMTMP/split.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam | grep -vP "@PG\tID:samtools" | wc -l | tr -d ' '
+  $ samtools view -F 4 $CRAMTMP/split.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam | grep -v "@PG	ID:samtools" | wc -l | tr -d ' '
   9
 
-  $ ID=$(samtools view -F 4 -H $CRAMTMP/split.test_test.bam | grep test_test | grep -vP "@PG\tID:samtools" | cut -f 2 | cut -f 2 -d ':')
-  $ samtools view -F 4 $CRAMTMP/split.test_test.bam | grep -vc ${ID} | grep -vP "@PG\tID:samtools" | tr -d ' '
+  $ ID=$(samtools view -F 4 -H $CRAMTMP/split.test_test.bam | grep test_test | grep -v "@PG	ID:samtools" | cut -f 2 | cut -f 2 -d ':')
+  $ samtools view -F 4 $CRAMTMP/split.test_test.bam | grep -vc ${ID} | grep -v "@PG	ID:samtools" | tr -d ' '
   0
-  $ samtools view -F 4 $CRAMTMP/split.test_test.bam | grep -vP "@PG\tID:samtools" | wc -l | tr -d ' '
+  $ samtools view -F 4 $CRAMTMP/split.test_test.bam | grep -v "@PG	ID:samtools" | wc -l | tr -d ' '
   11
 
-  $ ID=$(samtools view -F 4 -H $CRAMTMP/split.UCLA_1023.bam | grep UCLA_1023 | grep -vP "@PG\tID:samtools" | cut -f 2 | cut -f 2 -d ':')
-  $ samtools view -F 4 $CRAMTMP/split.UCLA_1023.bam | grep -vc ${ID} | grep -vP "@PG\tID:samtools" | tr -d ' '
+  $ ID=$(samtools view -F 4 -H $CRAMTMP/split.UCLA_1023.bam | grep UCLA_1023 | grep -v "@PG	ID:samtools" | cut -f 2 | cut -f 2 -d ':')
+  $ samtools view -F 4 $CRAMTMP/split.UCLA_1023.bam | grep -vc ${ID} | grep -v "@PG	ID:samtools" | tr -d ' '
   0
-  $ samtools view -F 4 $CRAMTMP/split.UCLA_1023.bam | grep -vP "@PG\tID:samtools" | wc -l | tr -d ' '
+  $ samtools view -F 4 $CRAMTMP/split.UCLA_1023.bam | grep -v "@PG	ID:samtools" | wc -l | tr -d ' '
   10
 
   $ $__PBTEST_PBMM2_EXE align $MERGED $REF $CRAMTMP/split_dataset.alignmentset.xml --split-by-sample
@@ -56,7 +56,7 @@ When both --split-by-sample and --sample were set, expect to see only one bam fi
   $ $__PBTEST_PBMM2_EXE align $REF $IN $CRAMTMP/splitsampleoverride.consensusalignmentset.xml --sort -j 8 --split-by-sample --sample "MySample" 2>&1 | fgrep -v 'Requested more threads'
   *Options --split-by-sample and --sample are mutually exclusive. Option --sample will be applied and --split-by-sample is ignored! (glob)
   $ [[ -f $CRAMTMP/splitsampleoverride.bam ]] || echo "File does not exist!"
-  $ samtools view -H $CRAMTMP/splitsampleoverride.bam | grep "@RG" | grep -vP "@PG\tID:samtools" | cut -f 6 | sort | uniq
+  $ samtools view -H $CRAMTMP/splitsampleoverride.bam | grep "@RG" | grep -v "@PG	ID:samtools" | cut -f 6 | sort | uniq
   SM:MySample
 
   $ $__PBTEST_PBMM2_EXE align --split-by-sample $NO_SM_BIOSAMPLES $REF $CRAMTMP/split-no-sm.bam
diff --git a/tests/cram/splitsamplejson.t b/tests/cram/splitsamplejson.t
@@ -28,22 +28,22 @@
   $ grep -c split_dataset_sorted_json.UCLA_1023.alignmentset.xml $CRAMTMP/split_dataset_sorted_json.json
   1
 
-  $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted_json.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam | grep 3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494 | grep -vP "@PG\tID:samtools" | cut -f 2 | cut -f 2 -d ':')
-  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam | grep -vc ${ID} | grep -vP "@PG\tID:samtools" | tr -d ' '
+  $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted_json.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam | grep 3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494 | grep -v "@PG	ID:samtools" | cut -f 2 | cut -f 2 -d ':')
+  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam | grep -vc ${ID} | grep -v "@PG	ID:samtools" | tr -d ' '
   0
-  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam | grep -vP "@PG\tID:samtools" | wc -l | tr -d ' '
+  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam | grep -v "@PG	ID:samtools" | wc -l | tr -d ' '
   9
 
-  $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted_json.test_test.bam | grep test_test | grep -vP "@PG\tID:samtools" | cut -f 2 | cut -f 2 -d ':')
-  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.test_test.bam | grep -vc ${ID} | grep -vP "@PG\tID:samtools" | tr -d ' '
+  $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted_json.test_test.bam | grep test_test | grep -v "@PG	ID:samtools" | cut -f 2 | cut -f 2 -d ':')
+  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.test_test.bam | grep -vc ${ID} | grep -v "@PG	ID:samtools" | tr -d ' '
   0
-  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.test_test.bam | grep -vP "@PG\tID:samtools" | wc -l | tr -d ' '
+  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.test_test.bam | grep -v "@PG	ID:samtools" | wc -l | tr -d ' '
   11
 
-  $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted_json.UCLA_1023.bam | grep UCLA_1023 | grep -vP "@PG\tID:samtools" | cut -f 2 | cut -f 2 -d ':')
-  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.UCLA_1023.bam | grep -vc ${ID} | grep -vP "@PG\tID:samtools" | tr -d ' '
+  $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted_json.UCLA_1023.bam | grep UCLA_1023 | grep -v "@PG	ID:samtools" | cut -f 2 | cut -f 2 -d ':')
+  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.UCLA_1023.bam | grep -vc ${ID} | grep -v "@PG	ID:samtools" | tr -d ' '
   0
-  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.UCLA_1023.bam | grep -vP "@PG\tID:samtools" | wc -l | tr -d ' '
+  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.UCLA_1023.bam | grep -v "@PG	ID:samtools" | wc -l | tr -d ' '
   10
 
   $ grep -c split_dataset_sorted_json.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.alignmentset.xml $CRAMTMP/split_dataset_sorted_json.json | tr -d ' '
diff --git a/tests/cram/splitsamplejsonsorted.t b/tests/cram/splitsamplejsonsorted.t
@@ -28,20 +28,20 @@
   $ grep -c split_dataset_sorted_json.UCLA_1023.alignmentset.xml $CRAMTMP/split_dataset_sorted_json.json
   1
 
-  $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted_json.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam | grep 3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494 | grep -vP "@PG\tID:samtools" | cut -f 2 | cut -f 2 -d ':')
-  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam | grep -vc ${ID} | grep -vP "@PG\tID:samtools" | tr -d ' '
+  $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted_json.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam | grep 3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494 | grep -v "@PG	ID:samtools" | cut -f 2 | cut -f 2 -d ':')
+  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam | grep -vc ${ID} | grep -v "@PG	ID:samtools" | tr -d ' '
   0
-  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam | grep -vP "@PG\tID:samtools" | wc -l | tr -d ' '
+  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam | grep -v "@PG	ID:samtools" | wc -l | tr -d ' '
   9
 
-  $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted_json.test_test.bam | grep test_test | grep -vP "@PG\tID:samtools" | cut -f 2 | cut -f 2 -d ':')
-  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.test_test.bam | grep -vc ${ID} | grep -vP "@PG\tID:samtools" | tr -d ' '
+  $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted_json.test_test.bam | grep test_test | grep -v "@PG	ID:samtools" | cut -f 2 | cut -f 2 -d ':')
+  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.test_test.bam | grep -vc ${ID} | grep -v "@PG	ID:samtools" | tr -d ' '
   0
-  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.test_test.bam | grep -vP "@PG\tID:samtools" | wc -l | tr -d ' '
+  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.test_test.bam | grep -v "@PG	ID:samtools" | wc -l | tr -d ' '
   11
 
-  $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted_json.UCLA_1023.bam | grep UCLA_1023 | grep -vP "@PG\tID:samtools" | cut -f 2 | cut -f 2 -d ':')
-  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.UCLA_1023.bam | grep -vc ${ID} | grep -vP "@PG\tID:samtools" | tr -d ' '
+  $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted_json.UCLA_1023.bam | grep UCLA_1023 | grep -v "@PG	ID:samtools" | cut -f 2 | cut -f 2 -d ':')
+  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.UCLA_1023.bam | grep -vc ${ID} | grep -v "@PG	ID:samtools" | tr -d ' '
   0
-  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.UCLA_1023.bam | grep -vP "@PG\tID:samtools" | wc -l | tr -d ' '
+  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.UCLA_1023.bam | grep -v "@PG	ID:samtools" | wc -l | tr -d ' '
   10
diff --git a/tests/cram/splitsamplesamename.t b/tests/cram/splitsamplesamename.t
@@ -6,22 +6,22 @@
   $ ls -l $CRAMTMP/splitname.*.bam | wc -l | tr -d ' '
   3
 
-  $ ID=$(samtools view -F 4 -H $CRAMTMP/splitname.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam | grep 3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494 | grep -vP "@PG\tID:samtools" | cut -f 2 | cut -f 2 -d ':')
-  $ samtools view -F 4 $CRAMTMP/splitname.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam | grep -vc ${ID} | grep -vP "@PG\tID:samtools" | tr -d ' '
+  $ ID=$(samtools view -F 4 -H $CRAMTMP/splitname.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam | grep 3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494 | grep -v "@PG	ID:samtools" | cut -f 2 | cut -f 2 -d ':')
+  $ samtools view -F 4 $CRAMTMP/splitname.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam | grep -vc ${ID} | grep -v "@PG	ID:samtools" | tr -d ' '
   0
-  $ samtools view -F 4 $CRAMTMP/splitname.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam | grep -vP "@PG\tID:samtools" | wc -l | tr -d ' '
+  $ samtools view -F 4 $CRAMTMP/splitname.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam | grep -v "@PG	ID:samtools" | wc -l | tr -d ' '
   9
 
-  $ ID=$(samtools view -F 4 -H $CRAMTMP/splitname.test-0.bam | grep "test(" | grep -vP "@PG\tID:samtools" | cut -f 2 | cut -f 2 -d ':')
-  $ samtools view -F 4 $CRAMTMP/splitname.test-0.bam | grep -vc ${ID} | grep -vP "@PG\tID:samtools" | tr -d ' '
+  $ ID=$(samtools view -F 4 -H $CRAMTMP/splitname.test-0.bam | grep "test(" | grep -v "@PG	ID:samtools" | cut -f 2 | cut -f 2 -d ':')
+  $ samtools view -F 4 $CRAMTMP/splitname.test-0.bam | grep -vc ${ID} | grep -v "@PG	ID:samtools" | tr -d ' '
   0
-  $ samtools view -F 4 $CRAMTMP/splitname.test-0.bam | grep -vP "@PG\tID:samtools" | wc -l | tr -d ' '
+  $ samtools view -F 4 $CRAMTMP/splitname.test-0.bam | grep -v "@PG	ID:samtools" | wc -l | tr -d ' '
   10
 
-  $ ID=$(samtools view -F 4 -H $CRAMTMP/splitname.test-1.bam | grep "test)" | grep -vP "@PG\tID:samtools" | cut -f 2 | cut -f 2 -d ':')
-  $ samtools view -F 4 $CRAMTMP/splitname.test-1.bam | grep -vc ${ID} | grep -vP "@PG\tID:samtools" | tr -d ' '
+  $ ID=$(samtools view -F 4 -H $CRAMTMP/splitname.test-1.bam | grep "test)" | grep -v "@PG	ID:samtools" | cut -f 2 | cut -f 2 -d ':')
+  $ samtools view -F 4 $CRAMTMP/splitname.test-1.bam | grep -vc ${ID} | grep -v "@PG	ID:samtools" | tr -d ' '
   0
-  $ samtools view -F 4 $CRAMTMP/splitname.test-1.bam | grep -vP "@PG\tID:samtools" | wc -l | tr -d ' '
+  $ samtools view -F 4 $CRAMTMP/splitname.test-1.bam | grep -v "@PG	ID:samtools" | wc -l | tr -d ' '
   11
 
   $ $__PBTEST_PBMM2_EXE align $MERGED $REF $CRAMTMP/split_dataset.alignmentset.xml --split-by-sample
diff --git a/tests/cram/splitsamplesorted.t b/tests/cram/splitsamplesorted.t
@@ -27,20 +27,20 @@
   $ grep -c split_dataset_sorted.UCLA_1023.alignmentset.xml $CRAMTMP/split_dataset_sorted.json
   1
 
-  $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam | grep 3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494 | grep -vP "@PG\tID:samtools" | cut -f 2 | cut -f 2 -d ':')
-  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam | grep -vc ${ID} | grep -vP "@PG\tID:samtools" | tr -d ' '
+  $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam | grep 3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494 | grep -v "@PG	ID:samtools" | cut -f 2 | cut -f 2 -d ':')
+  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam | grep -vc ${ID} | grep -v "@PG	ID:samtools" | tr -d ' '
   0
-  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam | grep -vP "@PG\tID:samtools" | wc -l | tr -d ' '
+  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam | grep -v "@PG	ID:samtools" | wc -l | tr -d ' '
   9
 
-  $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted.test_test.bam | grep test_test | grep -vP "@PG\tID:samtools" | cut -f 2 | cut -f 2 -d ':')
-  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted.test_test.bam | grep -vc ${ID} | grep -vP "@PG\tID:samtools" | tr -d ' '
+  $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted.test_test.bam | grep test_test | grep -v "@PG	ID:samtools" | cut -f 2 | cut -f 2 -d ':')
+  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted.test_test.bam | grep -vc ${ID} | grep -v "@PG	ID:samtools" | tr -d ' '
   0
-  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted.test_test.bam | grep -vP "@PG\tID:samtools" | wc -l | tr -d ' '
+  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted.test_test.bam | grep -v "@PG	ID:samtools" | wc -l | tr -d ' '
   11
 
-  $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted.UCLA_1023.bam | grep UCLA_1023 | grep -vP "@PG\tID:samtools" | cut -f 2 | cut -f 2 -d ':')
-  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted.UCLA_1023.bam | grep -vc ${ID} | grep -vP "@PG\tID:samtools" | tr -d ' '
+  $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted.UCLA_1023.bam | grep UCLA_1023 | grep -v "@PG	ID:samtools" | cut -f 2 | cut -f 2 -d ':')
+  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted.UCLA_1023.bam | grep -vc ${ID} | grep -v "@PG	ID:samtools" | tr -d ' '
   0
-  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted.UCLA_1023.bam | grep -vP "@PG\tID:samtools" | wc -l | tr -d ' '
+  $ samtools view -F 4 $CRAMTMP/split_dataset_sorted.UCLA_1023.bam | grep -v "@PG	ID:samtools" | wc -l | tr -d ' '
   10

Original file line number	Diff line number	Diff line change
`@@ -7,22 +7,22 @@`
`7`	`7`	`$ ls -l $CRAMTMP/split.*.bam \| wc -l \| tr -d ' '`
`8`	`8`	`3`
`9`	`9`
`10`		`- $ ID=$(samtools view -F 4 -H $CRAMTMP/split.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam \| grep 3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494 \| grep -vP "@PG\tID:samtools" \| cut -f 2 \| cut -f 2 -d ':')`
`11`		`- $ samtools view -F 4 $CRAMTMP/split.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam \| grep -vc ${ID} \| grep -vP "@PG\tID:samtools" \| tr -d ' '`
	`10`	`+ $ ID=$(samtools view -F 4 -H $CRAMTMP/split.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam \| grep 3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494 \| grep -v "@PG ID:samtools" \| cut -f 2 \| cut -f 2 -d ':')`
	`11`	`+ $ samtools view -F 4 $CRAMTMP/split.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam \| grep -vc ${ID} \| grep -v "@PG ID:samtools" \| tr -d ' '`
`12`	`12`	`0`
`13`		`- $ samtools view -F 4 $CRAMTMP/split.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam \| grep -vP "@PG\tID:samtools" \| wc -l \| tr -d ' '`
	`13`	`+ $ samtools view -F 4 $CRAMTMP/split.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam \| grep -v "@PG ID:samtools" \| wc -l \| tr -d ' '`
`14`	`14`	`9`
`15`	`15`
`16`		`- $ ID=$(samtools view -F 4 -H $CRAMTMP/split.test_test.bam \| grep test_test \| grep -vP "@PG\tID:samtools" \| cut -f 2 \| cut -f 2 -d ':')`
`17`		`- $ samtools view -F 4 $CRAMTMP/split.test_test.bam \| grep -vc ${ID} \| grep -vP "@PG\tID:samtools" \| tr -d ' '`
	`16`	`+ $ ID=$(samtools view -F 4 -H $CRAMTMP/split.test_test.bam \| grep test_test \| grep -v "@PG ID:samtools" \| cut -f 2 \| cut -f 2 -d ':')`
	`17`	`+ $ samtools view -F 4 $CRAMTMP/split.test_test.bam \| grep -vc ${ID} \| grep -v "@PG ID:samtools" \| tr -d ' '`
`18`	`18`	`0`
`19`		`- $ samtools view -F 4 $CRAMTMP/split.test_test.bam \| grep -vP "@PG\tID:samtools" \| wc -l \| tr -d ' '`
	`19`	`+ $ samtools view -F 4 $CRAMTMP/split.test_test.bam \| grep -v "@PG ID:samtools" \| wc -l \| tr -d ' '`
`20`	`20`	`11`
`21`	`21`
`22`		`- $ ID=$(samtools view -F 4 -H $CRAMTMP/split.UCLA_1023.bam \| grep UCLA_1023 \| grep -vP "@PG\tID:samtools" \| cut -f 2 \| cut -f 2 -d ':')`
`23`		`- $ samtools view -F 4 $CRAMTMP/split.UCLA_1023.bam \| grep -vc ${ID} \| grep -vP "@PG\tID:samtools" \| tr -d ' '`
	`22`	`+ $ ID=$(samtools view -F 4 -H $CRAMTMP/split.UCLA_1023.bam \| grep UCLA_1023 \| grep -v "@PG ID:samtools" \| cut -f 2 \| cut -f 2 -d ':')`
	`23`	`+ $ samtools view -F 4 $CRAMTMP/split.UCLA_1023.bam \| grep -vc ${ID} \| grep -v "@PG ID:samtools" \| tr -d ' '`
`24`	`24`	`0`
`25`		`- $ samtools view -F 4 $CRAMTMP/split.UCLA_1023.bam \| grep -vP "@PG\tID:samtools" \| wc -l \| tr -d ' '`
	`25`	`+ $ samtools view -F 4 $CRAMTMP/split.UCLA_1023.bam \| grep -v "@PG ID:samtools" \| wc -l \| tr -d ' '`
`26`	`26`	`10`
`27`	`27`
`28`	`28`	`$ $__PBTEST_PBMM2_EXE align $MERGED $REF $CRAMTMP/split_dataset.alignmentset.xml --split-by-sample`
`@@ -56,7 +56,7 @@ When both --split-by-sample and --sample were set, expect to see only one bam fi`
`56`	`56`	`$ $__PBTEST_PBMM2_EXE align $REF $IN $CRAMTMP/splitsampleoverride.consensusalignmentset.xml --sort -j 8 --split-by-sample --sample "MySample" 2>&1 \| fgrep -v 'Requested more threads'`
`57`	`57`	`*Options --split-by-sample and --sample are mutually exclusive. Option --sample will be applied and --split-by-sample is ignored! (glob)`
`58`	`58`	`$ [[ -f $CRAMTMP/splitsampleoverride.bam ]] \|\| echo "File does not exist!"`
`59`		`- $ samtools view -H $CRAMTMP/splitsampleoverride.bam \| grep "@RG" \| grep -vP "@PG\tID:samtools" \| cut -f 6 \| sort \| uniq`
	`59`	`+ $ samtools view -H $CRAMTMP/splitsampleoverride.bam \| grep "@RG" \| grep -v "@PG ID:samtools" \| cut -f 6 \| sort \| uniq`
`60`	`60`	`SM:MySample`
`61`	`61`
`62`	`62`	`$ $__PBTEST_PBMM2_EXE align --split-by-sample $NO_SM_BIOSAMPLES $REF $CRAMTMP/split-no-sm.bam`
Original file line number	Diff line number	Diff line change
`@@ -28,22 +28,22 @@`
`28`	`28`	`$ grep -c split_dataset_sorted_json.UCLA_1023.alignmentset.xml $CRAMTMP/split_dataset_sorted_json.json`
`29`	`29`	`1`
`30`	`30`
`31`		`- $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted_json.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam \| grep 3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494 \| grep -vP "@PG\tID:samtools" \| cut -f 2 \| cut -f 2 -d ':')`
`32`		`- $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam \| grep -vc ${ID} \| grep -vP "@PG\tID:samtools" \| tr -d ' '`
	`31`	`+ $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted_json.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam \| grep 3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494 \| grep -v "@PG ID:samtools" \| cut -f 2 \| cut -f 2 -d ':')`
	`32`	`+ $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam \| grep -vc ${ID} \| grep -v "@PG ID:samtools" \| tr -d ' '`
`33`	`33`	`0`
`34`		`- $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam \| grep -vP "@PG\tID:samtools" \| wc -l \| tr -d ' '`
	`34`	`+ $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam \| grep -v "@PG ID:samtools" \| wc -l \| tr -d ' '`
`35`	`35`	`9`
`36`	`36`
`37`		`- $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted_json.test_test.bam \| grep test_test \| grep -vP "@PG\tID:samtools" \| cut -f 2 \| cut -f 2 -d ':')`
`38`		`- $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.test_test.bam \| grep -vc ${ID} \| grep -vP "@PG\tID:samtools" \| tr -d ' '`
	`37`	`+ $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted_json.test_test.bam \| grep test_test \| grep -v "@PG ID:samtools" \| cut -f 2 \| cut -f 2 -d ':')`
	`38`	`+ $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.test_test.bam \| grep -vc ${ID} \| grep -v "@PG ID:samtools" \| tr -d ' '`
`39`	`39`	`0`
`40`		`- $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.test_test.bam \| grep -vP "@PG\tID:samtools" \| wc -l \| tr -d ' '`
	`40`	`+ $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.test_test.bam \| grep -v "@PG ID:samtools" \| wc -l \| tr -d ' '`
`41`	`41`	`11`
`42`	`42`
`43`		`- $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted_json.UCLA_1023.bam \| grep UCLA_1023 \| grep -vP "@PG\tID:samtools" \| cut -f 2 \| cut -f 2 -d ':')`
`44`		`- $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.UCLA_1023.bam \| grep -vc ${ID} \| grep -vP "@PG\tID:samtools" \| tr -d ' '`
	`43`	`+ $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted_json.UCLA_1023.bam \| grep UCLA_1023 \| grep -v "@PG ID:samtools" \| cut -f 2 \| cut -f 2 -d ':')`
	`44`	`+ $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.UCLA_1023.bam \| grep -vc ${ID} \| grep -v "@PG ID:samtools" \| tr -d ' '`
`45`	`45`	`0`
`46`		`- $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.UCLA_1023.bam \| grep -vP "@PG\tID:samtools" \| wc -l \| tr -d ' '`
	`46`	`+ $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.UCLA_1023.bam \| grep -v "@PG ID:samtools" \| wc -l \| tr -d ' '`
`47`	`47`	`10`
`48`	`48`
`49`	`49`	`$ grep -c split_dataset_sorted_json.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.alignmentset.xml $CRAMTMP/split_dataset_sorted_json.json \| tr -d ' '`
Original file line number	Diff line number	Diff line change
`@@ -28,20 +28,20 @@`
`28`	`28`	`$ grep -c split_dataset_sorted_json.UCLA_1023.alignmentset.xml $CRAMTMP/split_dataset_sorted_json.json`
`29`	`29`	`1`
`30`	`30`
`31`		`- $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted_json.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam \| grep 3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494 \| grep -vP "@PG\tID:samtools" \| cut -f 2 \| cut -f 2 -d ':')`
`32`		`- $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam \| grep -vc ${ID} \| grep -vP "@PG\tID:samtools" \| tr -d ' '`
	`31`	`+ $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted_json.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam \| grep 3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494 \| grep -v "@PG ID:samtools" \| cut -f 2 \| cut -f 2 -d ':')`
	`32`	`+ $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam \| grep -vc ${ID} \| grep -v "@PG ID:samtools" \| tr -d ' '`
`33`	`33`	`0`
`34`		`- $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam \| grep -vP "@PG\tID:samtools" \| wc -l \| tr -d ' '`
	`34`	`+ $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam \| grep -v "@PG ID:samtools" \| wc -l \| tr -d ' '`
`35`	`35`	`9`
`36`	`36`
`37`		`- $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted_json.test_test.bam \| grep test_test \| grep -vP "@PG\tID:samtools" \| cut -f 2 \| cut -f 2 -d ':')`
`38`		`- $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.test_test.bam \| grep -vc ${ID} \| grep -vP "@PG\tID:samtools" \| tr -d ' '`
	`37`	`+ $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted_json.test_test.bam \| grep test_test \| grep -v "@PG ID:samtools" \| cut -f 2 \| cut -f 2 -d ':')`
	`38`	`+ $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.test_test.bam \| grep -vc ${ID} \| grep -v "@PG ID:samtools" \| tr -d ' '`
`39`	`39`	`0`
`40`		`- $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.test_test.bam \| grep -vP "@PG\tID:samtools" \| wc -l \| tr -d ' '`
	`40`	`+ $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.test_test.bam \| grep -v "@PG ID:samtools" \| wc -l \| tr -d ' '`
`41`	`41`	`11`
`42`	`42`
`43`		`- $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted_json.UCLA_1023.bam \| grep UCLA_1023 \| grep -vP "@PG\tID:samtools" \| cut -f 2 \| cut -f 2 -d ':')`
`44`		`- $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.UCLA_1023.bam \| grep -vc ${ID} \| grep -vP "@PG\tID:samtools" \| tr -d ' '`
	`43`	`+ $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted_json.UCLA_1023.bam \| grep UCLA_1023 \| grep -v "@PG ID:samtools" \| cut -f 2 \| cut -f 2 -d ':')`
	`44`	`+ $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.UCLA_1023.bam \| grep -vc ${ID} \| grep -v "@PG ID:samtools" \| tr -d ' '`
`45`	`45`	`0`
`46`		`- $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.UCLA_1023.bam \| grep -vP "@PG\tID:samtools" \| wc -l \| tr -d ' '`
	`46`	`+ $ samtools view -F 4 $CRAMTMP/split_dataset_sorted_json.UCLA_1023.bam \| grep -v "@PG ID:samtools" \| wc -l \| tr -d ' '`
`47`	`47`	`10`
Original file line number	Diff line number	Diff line change
`@@ -6,22 +6,22 @@`
`6`	`6`	`$ ls -l $CRAMTMP/splitname.*.bam \| wc -l \| tr -d ' '`
`7`	`7`	`3`
`8`	`8`
`9`		`- $ ID=$(samtools view -F 4 -H $CRAMTMP/splitname.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam \| grep 3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494 \| grep -vP "@PG\tID:samtools" \| cut -f 2 \| cut -f 2 -d ':')`
`10`		`- $ samtools view -F 4 $CRAMTMP/splitname.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam \| grep -vc ${ID} \| grep -vP "@PG\tID:samtools" \| tr -d ' '`
	`9`	`+ $ ID=$(samtools view -F 4 -H $CRAMTMP/splitname.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam \| grep 3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494 \| grep -v "@PG ID:samtools" \| cut -f 2 \| cut -f 2 -d ':')`
	`10`	`+ $ samtools view -F 4 $CRAMTMP/splitname.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam \| grep -vc ${ID} \| grep -v "@PG ID:samtools" \| tr -d ' '`
`11`	`11`	`0`
`12`		`- $ samtools view -F 4 $CRAMTMP/splitname.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam \| grep -vP "@PG\tID:samtools" \| wc -l \| tr -d ' '`
	`12`	`+ $ samtools view -F 4 $CRAMTMP/splitname.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam \| grep -v "@PG ID:samtools" \| wc -l \| tr -d ' '`
`13`	`13`	`9`
`14`	`14`
`15`		`- $ ID=$(samtools view -F 4 -H $CRAMTMP/splitname.test-0.bam \| grep "test(" \| grep -vP "@PG\tID:samtools" \| cut -f 2 \| cut -f 2 -d ':')`
`16`		`- $ samtools view -F 4 $CRAMTMP/splitname.test-0.bam \| grep -vc ${ID} \| grep -vP "@PG\tID:samtools" \| tr -d ' '`
	`15`	`+ $ ID=$(samtools view -F 4 -H $CRAMTMP/splitname.test-0.bam \| grep "test(" \| grep -v "@PG ID:samtools" \| cut -f 2 \| cut -f 2 -d ':')`
	`16`	`+ $ samtools view -F 4 $CRAMTMP/splitname.test-0.bam \| grep -vc ${ID} \| grep -v "@PG ID:samtools" \| tr -d ' '`
`17`	`17`	`0`
`18`		`- $ samtools view -F 4 $CRAMTMP/splitname.test-0.bam \| grep -vP "@PG\tID:samtools" \| wc -l \| tr -d ' '`
	`18`	`+ $ samtools view -F 4 $CRAMTMP/splitname.test-0.bam \| grep -v "@PG ID:samtools" \| wc -l \| tr -d ' '`
`19`	`19`	`10`
`20`	`20`
`21`		`- $ ID=$(samtools view -F 4 -H $CRAMTMP/splitname.test-1.bam \| grep "test)" \| grep -vP "@PG\tID:samtools" \| cut -f 2 \| cut -f 2 -d ':')`
`22`		`- $ samtools view -F 4 $CRAMTMP/splitname.test-1.bam \| grep -vc ${ID} \| grep -vP "@PG\tID:samtools" \| tr -d ' '`
	`21`	`+ $ ID=$(samtools view -F 4 -H $CRAMTMP/splitname.test-1.bam \| grep "test)" \| grep -v "@PG ID:samtools" \| cut -f 2 \| cut -f 2 -d ':')`
	`22`	`+ $ samtools view -F 4 $CRAMTMP/splitname.test-1.bam \| grep -vc ${ID} \| grep -v "@PG ID:samtools" \| tr -d ' '`
`23`	`23`	`0`
`24`		`- $ samtools view -F 4 $CRAMTMP/splitname.test-1.bam \| grep -vP "@PG\tID:samtools" \| wc -l \| tr -d ' '`
	`24`	`+ $ samtools view -F 4 $CRAMTMP/splitname.test-1.bam \| grep -v "@PG ID:samtools" \| wc -l \| tr -d ' '`
`25`	`25`	`11`
`26`	`26`
`27`	`27`	`$ $__PBTEST_PBMM2_EXE align $MERGED $REF $CRAMTMP/split_dataset.alignmentset.xml --split-by-sample`
Original file line number	Diff line number	Diff line change
`@@ -27,20 +27,20 @@`
`27`	`27`	`$ grep -c split_dataset_sorted.UCLA_1023.alignmentset.xml $CRAMTMP/split_dataset_sorted.json`
`28`	`28`	`1`
`29`	`29`
`30`		`- $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam \| grep 3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494 \| grep -vP "@PG\tID:samtools" \| cut -f 2 \| cut -f 2 -d ':')`
`31`		`- $ samtools view -F 4 $CRAMTMP/split_dataset_sorted.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam \| grep -vc ${ID} \| grep -vP "@PG\tID:samtools" \| tr -d ' '`
	`30`	`+ $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam \| grep 3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494 \| grep -v "@PG ID:samtools" \| cut -f 2 \| cut -f 2 -d ':')`
	`31`	`+ $ samtools view -F 4 $CRAMTMP/split_dataset_sorted.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam \| grep -vc ${ID} \| grep -v "@PG ID:samtools" \| tr -d ' '`
`32`	`32`	`0`
`33`		`- $ samtools view -F 4 $CRAMTMP/split_dataset_sorted.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam \| grep -vP "@PG\tID:samtools" \| wc -l \| tr -d ' '`
	`33`	`+ $ samtools view -F 4 $CRAMTMP/split_dataset_sorted.3260208_188nM-GTAC_2xGCratio_LP7_100fps_15min_5kEColi_SP2p1_3uMSSB_BA243494.bam \| grep -v "@PG ID:samtools" \| wc -l \| tr -d ' '`
`34`	`34`	`9`
`35`	`35`
`36`		`- $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted.test_test.bam \| grep test_test \| grep -vP "@PG\tID:samtools" \| cut -f 2 \| cut -f 2 -d ':')`
`37`		`- $ samtools view -F 4 $CRAMTMP/split_dataset_sorted.test_test.bam \| grep -vc ${ID} \| grep -vP "@PG\tID:samtools" \| tr -d ' '`
	`36`	`+ $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted.test_test.bam \| grep test_test \| grep -v "@PG ID:samtools" \| cut -f 2 \| cut -f 2 -d ':')`
	`37`	`+ $ samtools view -F 4 $CRAMTMP/split_dataset_sorted.test_test.bam \| grep -vc ${ID} \| grep -v "@PG ID:samtools" \| tr -d ' '`
`38`	`38`	`0`
`39`		`- $ samtools view -F 4 $CRAMTMP/split_dataset_sorted.test_test.bam \| grep -vP "@PG\tID:samtools" \| wc -l \| tr -d ' '`
	`39`	`+ $ samtools view -F 4 $CRAMTMP/split_dataset_sorted.test_test.bam \| grep -v "@PG ID:samtools" \| wc -l \| tr -d ' '`
`40`	`40`	`11`
`41`	`41`
`42`		`- $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted.UCLA_1023.bam \| grep UCLA_1023 \| grep -vP "@PG\tID:samtools" \| cut -f 2 \| cut -f 2 -d ':')`
`43`		`- $ samtools view -F 4 $CRAMTMP/split_dataset_sorted.UCLA_1023.bam \| grep -vc ${ID} \| grep -vP "@PG\tID:samtools" \| tr -d ' '`
	`42`	`+ $ ID=$(samtools view -F 4 -H $CRAMTMP/split_dataset_sorted.UCLA_1023.bam \| grep UCLA_1023 \| grep -v "@PG ID:samtools" \| cut -f 2 \| cut -f 2 -d ':')`
	`43`	`+ $ samtools view -F 4 $CRAMTMP/split_dataset_sorted.UCLA_1023.bam \| grep -vc ${ID} \| grep -v "@PG ID:samtools" \| tr -d ' '`
`44`	`44`	`0`
`45`		`- $ samtools view -F 4 $CRAMTMP/split_dataset_sorted.UCLA_1023.bam \| grep -vP "@PG\tID:samtools" \| wc -l \| tr -d ' '`
	`45`	`+ $ samtools view -F 4 $CRAMTMP/split_dataset_sorted.UCLA_1023.bam \| grep -v "@PG ID:samtools" \| wc -l \| tr -d ' '`
`46`	`46`	`10`