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CNV analysis: coverage profile is now re-created every time
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@Ott-Alexander
Ott-Alexander committed Sep 10, 2024
1 parent 0d724e2 commit 36e103e
Showing 1 changed file with 25 additions and 61 deletions.
86 changes: 25 additions & 61 deletions src/Pipelines/somatic_dna.php
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Original file line number Diff line number Diff line change
Expand Up @@ -783,41 +783,22 @@ function($str) { return explode("\t", $str); },
$ref_file_t = "{$ref_folder_t}/{$t_id}.cov";
$ref_file_t_off_target = "{$ref_folder_t_off_target}/{$t_id}.cov";

if(!file_exists($ref_file_t) )
{
$parser->exec(get_path("ngs-bits")."BedCoverage", "-clear -min_mapq 0 -decimals 4 -bam $t_bam -in $target_bed -out $t_cov -threads {$threads} -ref {$ref_genome}",true);
$parser->exec(get_path("ngs-bits")."BedSort", "-uniq -in $t_cov -out $t_cov",true);
}
else
{
$t_cov = $ref_file_t;
}

if( !file_exists($ref_file_t_off_target ) )
{
$parser->exec(get_path("ngs-bits")."BedCoverage", "-clear -min_mapq 10 -decimals 4 -in $off_target_bed -bam $t_bam -out $t_cov_off_target -threads {$threads} -ref {$ref_genome}",true);
$parser->exec(get_path("ngs-bits")."BedSort", "-uniq -in $t_cov_off_target -out $t_cov_off_target",true);
}
else
{
$t_cov_off_target = $ref_file_t_off_target;
}
$parser->exec(get_path("ngs-bits")."BedCoverage", "-clear -min_mapq 0 -decimals 4 -bam $t_bam -in $target_bed -out $t_cov -threads {$threads} -ref {$ref_genome}",true);
$parser->exec(get_path("ngs-bits")."BedSort", "-uniq -in $t_cov -out $t_cov",true);

$parser->exec(get_path("ngs-bits")."BedCoverage", "-clear -min_mapq 10 -decimals 4 -in $off_target_bed -bam $t_bam -out $t_cov_off_target -threads {$threads} -ref {$ref_genome}",true);
$parser->exec(get_path("ngs-bits")."BedSort", "-uniq -in $t_cov_off_target -out $t_cov_off_target",true);


//copy tumor sample coverage file to reference folder (has to be done before ClinCNV call to avoid analyzing the same sample twice)
if (db_is_enabled("NGSD") && is_valid_ref_tumor_sample_for_cnv_analysis($t_id))
{
//copy file
if(!file_exists($ref_file_t)) //Do not overwrite existing reference files in cov folder
{
$parser->copyFile($t_cov, $ref_file_t);
$t_cov = $ref_file_t;
}

if(!file_exists($ref_file_t_off_target))
{
$parser->copyFile($t_cov_off_target,$ref_file_t_off_target);
$t_cov_off_target = $ref_file_t_off_target;
}
$parser->log("Moving tumor sample coverage file to reference folder...");
$parser->copyFile($t_cov, $ref_file_t);
$t_cov = $ref_file_t;

$parser->copyFile($t_cov_off_target,$ref_file_t_off_target);
$t_cov_off_target = $ref_file_t_off_target;
}

if (!$single_sample)
Expand All @@ -828,41 +809,24 @@ function($str) { return explode("\t", $str); },
$ref_file_n = $ref_folder_n."/".$n_id.".cov";
$ref_file_n_off_target = "{$ref_folder_n_off_target}/{$n_id}.cov";

if(!file_exists($ref_file_n))
{
$parser->exec(get_path("ngs-bits")."BedCoverage", "-clear -min_mapq 0 -decimals 4 -bam $n_bam -in $target_bed -out $n_cov -threads {$threads} -ref {$ref_genome}", true);
$parser->exec(get_path("ngs-bits")."BedSort", "-uniq -in $n_cov -out $n_cov",true);
}
else
{
$n_cov = $ref_file_n;
}

if(!file_exists($ref_file_n_off_target) )
{
$parser->exec(get_path("ngs-bits")."BedCoverage", "-clear -min_mapq 10 -decimals 4 -in $off_target_bed -bam $n_bam -out $n_cov_off_target -threads {$threads} -ref {$ref_genome}",true);
$parser->exec(get_path("ngs-bits")."BedSort", "-uniq -in $n_cov_off_target -out $n_cov_off_target",true);
}
else
{
$n_cov_off_target = $ref_file_n_off_target;
}
$parser->exec(get_path("ngs-bits")."BedCoverage", "-clear -min_mapq 0 -decimals 4 -bam $n_bam -in $target_bed -out $n_cov -threads {$threads} -ref {$ref_genome}", true);
$parser->exec(get_path("ngs-bits")."BedSort", "-uniq -in $n_cov -out $n_cov",true);

$parser->exec(get_path("ngs-bits")."BedCoverage", "-clear -min_mapq 10 -decimals 4 -in $off_target_bed -bam $n_bam -out $n_cov_off_target -threads {$threads} -ref {$ref_genome}",true);
$parser->exec(get_path("ngs-bits")."BedSort", "-uniq -in $n_cov_off_target -out $n_cov_off_target",true);


// copy normal sample coverage file to reference folder (only if valid and not yet there).
if (db_is_enabled("NGSD") && is_valid_ref_sample_for_cnv_analysis($n_id))
{
//copy file
if (!file_exists($ref_file_n)) //do not overwrite existing coverage files in ref folder
{
$parser->copyFile($n_cov, $ref_file_n);
$n_cov = $ref_file_n;
}

if(!file_exists($ref_file_n_off_target))
{
$parser->copyFile($n_cov_off_target, $ref_file_n_off_target);
$n_cov_off_target = $ref_file_n_off_target;
}
$parser->log("Moving normal sample coverage file to reference folder...");
$parser->copyFile($n_cov, $ref_file_n);
$n_cov = $ref_file_n;

$parser->copyFile($n_cov_off_target, $ref_file_n_off_target);
$n_cov_off_target = $ref_file_n_off_target;

}
}

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