[BFX-534] Update cram tests for mm2.26

PacificBiosciences · Aug 14, 2023 · bcd99f5 · bcd99f5
1 parent a193c7b
commit bcd99f5
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Showing 7 changed files with 25 additions and 30 deletions.
diff --git a/tests/cram/best_n.t b/tests/cram/best_n.t
@@ -1,34 +1,33 @@
 Basic functionality of option `-N <int>`
 
   $ "$PBMM2" align -j 1 --preset HiFi \
-  > "$TESTDIR"/data/r64385e_20230505_214554_B01.141297211.bc2049--bc2049.reference.fasta \
-  > "$TESTDIR"/data/r64385e_20230505_214554_B01.141297211.bc2049--bc2049.bam \
+  > "$TESTDIR"/data/r64385e_20230505_214554_B01.73859681.bc2049--bc2049.reference.fasta \
+  > "$TESTDIR"/data/r64385e_20230505_214554_B01.73859681.bc2049--bc2049.bam \
   > out.bam
 
   $ samtools view out.bam | cut -f 1-5 | sed 's/\t/ /g'
-  m64385e_230506_131841/141297211/ccs 0 chr4 5061 60
-  m64385e_230506_131841/141297211/ccs 2048 chr4 8476 60
-  m64385e_230506_131841/141297211/ccs 2064 chr16 11579 1
-  m64385e_230506_131841/141297211/ccs 2064 chr16 11681 60
-  m64385e_230506_131841/141297211/ccs 2064 chr16 12205 14
-  m64385e_230506_131841/141297211/ccs 2064 chr16 12060 12
-  m64385e_230506_131841/141297211/ccs 2064 chr16 11846 22
+  m64385e_230506_131841/73859681/ccs 16 chr12 14240 60
+  m64385e_230506_131841/73859681/ccs 2064 chr12 14239 60
+  m64385e_230506_131841/73859681/ccs 2048 chr12 14434 60
+  m64385e_230506_131841/73859681/ccs 2064 chr12 14946 60
+  m64385e_230506_131841/73859681/ccs 2048 chr12 16876 60
+  m64385e_230506_131841/73859681/ccs 2048 chr12 14245 60
 
   $ "$PBMM2" align -j 1 --preset HiFi -N 1 \
-  > "$TESTDIR"/data/r64385e_20230505_214554_B01.141297211.bc2049--bc2049.reference.fasta \
-  > "$TESTDIR"/data/r64385e_20230505_214554_B01.141297211.bc2049--bc2049.bam \
+  > "$TESTDIR"/data/r64385e_20230505_214554_B01.73859681.bc2049--bc2049.reference.fasta \
+  > "$TESTDIR"/data/r64385e_20230505_214554_B01.73859681.bc2049--bc2049.bam \
   > out.n1.bam
 
   $ samtools view out.n1.bam | cut -f 1-5 | sed 's/\t/ /g'
-  m64385e_230506_131841/141297211/ccs 0 chr4 5061 60
+  m64385e_230506_131841/73859681/ccs 16 chr12 14240 60
 
   $ "$PBMM2" align -j 1 --preset HiFi -N 4 \
-  > "$TESTDIR"/data/r64385e_20230505_214554_B01.141297211.bc2049--bc2049.reference.fasta \
-  > "$TESTDIR"/data/r64385e_20230505_214554_B01.141297211.bc2049--bc2049.bam \
+  > "$TESTDIR"/data/r64385e_20230505_214554_B01.73859681.bc2049--bc2049.reference.fasta \
+  > "$TESTDIR"/data/r64385e_20230505_214554_B01.73859681.bc2049--bc2049.bam \
   > out.n4.bam
 
   $ samtools view out.n4.bam | cut -f 1-5 | sed 's/\t/ /g'
-  m64385e_230506_131841/141297211/ccs 0 chr4 5061 60
-  m64385e_230506_131841/141297211/ccs 2048 chr4 8476 60
-  m64385e_230506_131841/141297211/ccs 2064 chr16 11579 1
-  m64385e_230506_131841/141297211/ccs 2064 chr16 11681 60
+  m64385e_230506_131841/73859681/ccs 16 chr12 14240 60
+  m64385e_230506_131841/73859681/ccs 2064 chr12 14239 60
+  m64385e_230506_131841/73859681/ccs 2048 chr12 14434 60
+  m64385e_230506_131841/73859681/ccs 2064 chr12 14946 60
diff --git a/tests/cram/data/r64385e_20230505_214554_B01.141297211.bc2049--bc2049.bam b/tests/cram/data/r64385e_20230505_214554_B01.141297211.bc2049--bc2049.bam
diff --git a/tests/cram/data/r64385e_20230505_214554_B01.141297211.bc2049--bc2049.reference.fasta b/tests/cram/data/r64385e_20230505_214554_B01.141297211.bc2049--bc2049.reference.fasta
diff --git a/tests/cram/data/r64385e_20230505_214554_B01.73859681.bc2049--bc2049.bam b/tests/cram/data/r64385e_20230505_214554_B01.73859681.bc2049--bc2049.bam
diff --git a/tests/cram/data/r64385e_20230505_214554_B01.73859681.bc2049--bc2049.reference.fasta b/tests/cram/data/r64385e_20230505_214554_B01.73859681.bc2049--bc2049.reference.fasta
diff --git a/tests/cram/rmt.t b/tests/cram/rmt.t
@@ -1,12 +1,12 @@
 Repeated matches trimming tags all alignments of a record with `rm:i:1` if there is at least one overlap in query positions
 
   $ "$PBMM2" align -j 1 --preset HiFi \
-  > "$TESTDIR"/data/r64385e_20230505_214554_B01.141297211.bc2049--bc2049.reference.fasta \
-  > "$TESTDIR"/data/r64385e_20230505_214554_B01.141297211.bc2049--bc2049.bam \
+  > "$TESTDIR"/data/r64385e_20230505_214554_B01.73859681.bc2049--bc2049.reference.fasta \
+  > "$TESTDIR"/data/r64385e_20230505_214554_B01.73859681.bc2049--bc2049.bam \
   > out.bam
 
   $ samtools view -c out.bam
-  7
+  6
 
   $ samtools view out.bam | grep -c -o "rm:i:1"
-  7
+  6
diff --git a/tests/meson.build b/tests/meson.build
@@ -38,7 +38,7 @@ pbmm2_cram_test = [
   'baminput_28',
   'baminput_29',
   'baminput_30',
-  # 'best_n',
+  'best_n',
   'biosampleConsensus_1',
   'biosampleConsensus_2',
   'biosampleConsensus_3',
@@ -105,7 +105,7 @@ pbmm2_cram_test = [
   'rc_ubam_ml',
   'readgroup',
   'refxml',
-  # 'rmt',
+  'rmt',
   'sa_1',
   'sa_2',
   'splitsample',