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Merge pull request #29 from cancerit/dev
Modified behaviour for commandline assembly and species. Looks good
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,23 +1,23 @@ | ||
| package Sanger::CGP::Pindel::OutputGen::BamUtil; | ||
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| ########## LICENCE ########## | ||
| # Copyright (c) 2014 Genome Research Ltd. | ||
| # | ||
| # Author: Keiran Raine <[email protected]> | ||
| # | ||
| # Copyright (c) 2014 Genome Research Ltd. | ||
| # | ||
| # Author: Keiran Raine <[email protected]> | ||
| # | ||
| # This file is part of cgpPindel. | ||
| # | ||
| # cgpPindel is free software: you can redistribute it and/or modify it under | ||
| # the terms of the GNU Affero General Public License as published by the Free | ||
| # Software Foundation; either version 3 of the License, or (at your option) any | ||
| # later version. | ||
| # | ||
| # This program is distributed in the hope that it will be useful, but WITHOUT | ||
| # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS | ||
| # FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more | ||
| # details. | ||
| # | ||
| # You should have received a copy of the GNU Affero General Public License | ||
| # | ||
| # cgpPindel is free software: you can redistribute it and/or modify it under | ||
| # the terms of the GNU Affero General Public License as published by the Free | ||
| # Software Foundation; either version 3 of the License, or (at your option) any | ||
| # later version. | ||
| # | ||
| # This program is distributed in the hope that it will be useful, but WITHOUT | ||
| # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS | ||
| # FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more | ||
| # details. | ||
| # | ||
| # You should have received a copy of the GNU Affero General Public License | ||
| # along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
| ########## LICENCE ########## | ||
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@@ -107,7 +107,7 @@ sub parse_contigs{ | |
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| if(defined $man_species) { | ||
| if(defined $species) { | ||
| die "ERROR: Manually entered species ($man_species) doesn't match BAM file header ($species)\n" | ||
| warn "WARN: Manually entered species ($man_species) doesn't match BAM file header ($species). Defaulting to BAM header species.\n" | ||
| if($man_species ne $species); | ||
| } | ||
| else { $species = $man_species; } | ||
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@@ -116,7 +116,7 @@ sub parse_contigs{ | |
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| if(defined $man_assembly) { | ||
| if(defined $assembly) { | ||
| die "ERROR: Manually entered assembly ($man_assembly) doesn't match BAM file header ($assembly)\n" | ||
| warn "WARN: Manually entered assembly ($man_assembly) doesn't match BAM file header ($assembly). Defaulting to BAM header assembly.\n" | ||
| if($man_assembly ne $assembly); | ||
| } | ||
| else { $assembly = $man_assembly; } | ||
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