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Speed up BAM, CRAM 3.1 and 4.0 testing in test/test.pl's test_view. #1308

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Speed up BAM, CRAM 3.1 and 4.0 testing in test/test.pl's test_view. #1308

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141 changes: 64 additions & 77 deletions test/test.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -520,6 +520,32 @@ sub test_view
my ($opts, $nthreads) = @_;
my $tv_args = $nthreads ? "-\@$nthreads" : "";

# Files appropriate for CRAM V3.1 and V4.0 testing
my %cram31 = ("auxf#values.sam" => 1,
"c1#pad3.sam" => 1,
"ce#5.sam" => 1,
"ce#1000.sam", => 1,
"ce#large_seq.sam", => 1,
"ce#supp.sam", => 1,
"xx#MD.sam", => 1,
"xx#blank.sam", => 1,
"xx#large_aux.sam", => 1,
"xx#pair.sam", => 1,
"xx#tlen.sam" => 1);

# Files appropriate for CRAM multi-ref containers
my %cram_ms = ("ce#1000.sam" => 1,
"ce#5.sam" => 1,
"ce#5b.sam" => 1,
"ce#unmap.sam" => 1,
"ce#unmap1.sam" => 1,
"ce#unmap2.sam" => 1,
"xx#blank.sam" => 1,
"xx#minimal.sam" => 1,
"xx#tlen.sam" => 1,
"xx#tlen2.sam" => 1,
"xx#triplet.sam" => 1);

foreach my $sam (glob("*#*.sam")) {
my ($base, $ref) = ($sam =~ /((.*)#.*)\.sam/);
$ref .= ".fa";
Expand All @@ -536,9 +562,11 @@ sub test_view
$test_view_failures = 0;

# SAM -> BAM -> SAM
testv $opts, "./test_view $tv_args -S -b $sam > $bam";
testv $opts, "./test_view $tv_args $bam > $bam.sam_";
testv $opts, "./compare_sam.pl $sam $bam.sam_";
if ($sam eq "ce#1000.sam") {
testv $opts, "./test_view $tv_args -S -b $sam > $bam";
testv $opts, "./test_view $tv_args $bam > $bam.sam_";
testv $opts, "./compare_sam.pl $sam $bam.sam_";
}

# SAM -> BAMu -> SAM
testv $opts, "./test_view $tv_args -S -l0 -b $sam > $bam";
Expand All @@ -550,93 +578,52 @@ sub test_view
testv $opts, "./test_view $tv_args -D $cram > $cram.sam_";
testv $opts, "./compare_sam.pl $md $sam $cram.sam_";

# BAM -> CRAM2 -> BAM -> SAM
$cram = "$bam.cram";
testv $opts, "./test_view $tv_args -t $ref -C -o VERSION=2.1 $bam > $cram";
testv $opts, "./test_view $tv_args -b -D $cram > $cram.bam";
testv $opts, "./test_view $tv_args $cram.bam > $cram.bam.sam_";
testv $opts, "./compare_sam.pl $md $sam $cram.bam.sam_";

# SAM -> CRAM3u -> SAM
$cram = "$base.tmp.cram";
testv $opts, "./test_view $tv_args -t $ref -S -l0 -C -o VERSION=3.0 $sam > $cram";
testv $opts, "./test_view $tv_args -D $cram > $cram.sam_";
testv $opts, "./compare_sam.pl $md $sam $cram.sam_";

# BAM -> CRAM3 -> BAM -> SAM
$cram = "$bam.cram";
testv $opts, "./test_view $tv_args -t $ref -C -o VERSION=3.0 $bam > $cram";
testv $opts, "./test_view $tv_args -b -D $cram > $cram.bam";
testv $opts, "./test_view $tv_args $cram.bam > $cram.bam.sam_";
testv $opts, "./compare_sam.pl $md $sam $cram.bam.sam_";

# CRAM3 -> CRAM2
$cram = "$base.tmp.cram";
testv $opts, "./test_view $tv_args -t $ref -C -o VERSION=2.1 $cram > $cram.cram";

# CRAM2 -> CRAM3
testv $opts, "./test_view $tv_args -t $ref -C -o VERSION=3.0 $cram.cram > $cram";

# CRAM3 -> CRAM3 + multi-slice
testv $opts, "./test_view $tv_args -t $ref -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 $cram.cram > $cram";
testv $opts, "./test_view $tv_args $cram > $cram.sam_";
testv $opts, "./compare_sam.pl $md $sam $cram.sam_";

## Experimental CRAM 3.1 support.
# SAM -> CRAM31u -> SAM
foreach my $profile (qw/fast normal small archive/) {
if ($sam eq "ce#1000.sam") {
$cram = "$base.tmp.cram";
testv $opts, "./test_view $tv_args -t $ref -S -l7 -C -o VERSION=3.1 -o $profile $sam > $cram";
testv $opts, "./test_view $tv_args -t $ref -S -l0 -C -o VERSION=3.0 $sam > $cram";
testv $opts, "./test_view $tv_args -D $cram > $cram.sam_";
testv $opts, "./compare_sam.pl $md $sam $cram.sam_";
}

# BAM -> CRAM31 -> BAM -> SAM
# BAM -> CRAM3 -> SAM
$cram = "$bam.cram";
testv $opts, "./test_view $tv_args -t $ref -C -o VERSION=3.1 $bam > $cram";
testv $opts, "./test_view $tv_args -b -D $cram > $cram.bam";
testv $opts, "./test_view $tv_args $cram.bam > $cram.bam.sam_";
testv $opts, "./test_view $tv_args -t $ref -C -o VERSION=3.0 $bam > $cram";
testv $opts, "./test_view $tv_args $cram > $cram.bam.sam_";
testv $opts, "./compare_sam.pl $md $sam $cram.bam.sam_";

# CRAM31 -> CRAM30
$cram = "$base.tmp.cram";
testv $opts, "./test_view $tv_args -t $ref -C -o VERSION=3.0 $cram > $cram.cram";

# CRAM30 -> CRAM31
testv $opts, "./test_view $tv_args -t $ref -C -o VERSION=3.1 $cram.cram > $cram";

# CRAM31 -> CRAM31 + multi-slice
testv $opts, "./test_view $tv_args -t $ref -C -o VERSION=3.1 -o seqs_per_slice=7 -o slices_per_container=5 $cram.cram > $cram";
testv $opts, "./test_view $tv_args $cram > $cram.sam_";
testv $opts, "./compare_sam.pl $md $sam $cram.sam_";

## Experimental CRAM 4.0 support.
# SAM -> CRAM40u -> SAM
foreach my $profile (qw/fast normal small archive/) {
$cram = "$base.tmp.cram";
testv $opts, "./test_view $tv_args -t $ref -S -l7 -C -o VERSION=4.0 -o $profile $sam > $cram";
testv $opts, "./test_view $tv_args -D $cram > $cram.sam_";
# CRAM3 -> CRAM3 + multi-slice
if (exists($cram_ms{$sam}) && $nthreads > 0) {
testv $opts, "./test_view $tv_args -t $ref -C -o VERSION=3.0 -o seqs_per_slice=7 -o slices_per_container=5 $cram > $cram.ms";
testv $opts, "./test_view $tv_args $cram.ms > $cram.sam_";
testv $opts, "./compare_sam.pl $md $sam $cram.sam_";
}

# BAM -> CRAM40 -> BAM -> SAM
$cram = "$bam.cram";
testv $opts, "./test_view $tv_args -t $ref -C -o VERSION=4.0 $bam > $cram";
testv $opts, "./test_view $tv_args -b -D $cram > $cram.bam";
testv $opts, "./test_view $tv_args $cram.bam > $cram.bam.sam_";
testv $opts, "./compare_sam.pl $md $sam $cram.bam.sam_";

# CRAM40 -> CRAM30
$cram = "$base.tmp.cram";
testv $opts, "./test_view $tv_args -t $ref -C -o VERSION=3.0 $cram > $cram.cram";

# CRAM30 -> CRAM40
testv $opts, "./test_view $tv_args -t $ref -C -o VERSION=4.0 $cram.cram > $cram";
if (exists($cram31{$sam}) && $nthreads > 0) {
## Experimental CRAM 3.1 support.
# SAM -> CRAM31 -> SAM
my @p = $sam eq "ce#1000.sam"
? (qw/fast normal small archive/)
: (qw/archive/);
foreach my $profile (@p) {
$cram = "$base.tmp.cram";
testv $opts, "./test_view $tv_args -t $ref -S -l7 -C -o VERSION=3.1 -o $profile $sam > $cram";
testv $opts, "./test_view $tv_args -D $cram > $cram.sam_";
testv $opts, "./compare_sam.pl $md $sam $cram.sam_";
}

# CRAM40 -> CRAM40 + multi-slice
testv $opts, "./test_view $tv_args -t $ref -C -o VERSION=4.0 -o seqs_per_slice=7 -o slices_per_container=5 $cram.cram > $cram";
testv $opts, "./test_view $tv_args $cram > $cram.sam_";
testv $opts, "./compare_sam.pl $md $sam $cram.sam_";
## Experimental CRAM 4.0 support.
# SAM -> CRAM40 -> SAM
my @p = $sam eq "ce#large_seq.sam" || $sam eq "xx#large_aux.sam"
? (qw/fast normal small archive/)
: (qw/archive/);
foreach my $profile (@p) {
$cram = "$base.tmp.cram";
testv $opts, "./test_view $tv_args -t $ref -S -l7 -C -o VERSION=4.0 -o $profile $sam > $cram";
testv $opts, "./test_view $tv_args -D $cram > $cram.sam_";
testv $opts, "./compare_sam.pl $md $sam $cram.sam_";
}
}

# Java pre-made CRAM -> SAM
my $jcram = "${base}_java.cram";
Expand Down