minor bugfix to blast parser

the orientation of the alignment was not correctly reported. HLAminer does not use this information and thus is NOT affected by the change.
bcgsc · Oct 10, 2017 · dc6fe18 · dc6fe18
1 parent 2a7b01e
commit dc6fe18
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Showing 6 changed files with 8 additions and 8 deletions.
diff --git a/HLAminer_v1-3-1.tar.gz b/HLAminer_v1-3-1.tar.gz
diff --git a/HLAminer_v1.3.1/bin/parseXMLblast.old b/HLAminer_v1.3.1/bin/parseXMLblast.old
@@ -81,7 +81,7 @@ while( my $result = $in->next_result ) {
       if ($identity >= $id_cutoff)
       {
 
-        if($hsp->query->strand == -1 ){
+        if($hsp->hit->strand == -1 ){
              $direct="-";
         }else{
              $direct="+";

diff --git a/HLAminer_v1.3.1/bin/parseXMLblast.pl b/HLAminer_v1.3.1/bin/parseXMLblast.pl
@@ -100,7 +100,7 @@
       if ($identity >= $id_cutoff)
       {
 
-        if($hsp->query->strand == -1 ){
+        if($hsp->hit->strand < 1 ){
              $direct="-";
         }else{
              $direct="+";

diff --git a/HLAminer_v1.3.1/bin/parseXMLblast_v1-1.pl b/HLAminer_v1.3.1/bin/parseXMLblast_v1-1.pl
@@ -83,7 +83,7 @@
       if ($identity >= $id_cutoff)
       {
 
-        if($hsp->query->strand == -1 ){
+        if($hsp->hit->strand == -1 ){
              $direct="-";
         }else{
              $direct="+";

diff --git a/HLAminer_v1.3.1/bin/parseXMLblast_v1-2.pl b/HLAminer_v1.3.1/bin/parseXMLblast_v1-2.pl
@@ -94,7 +94,7 @@
       if ($identity >= $id_cutoff)
       {
 
-        if($hsp->query->strand == -1 ){
+        if($hsp->hit->strand == -1 ){
              $direct="-";
         }else{
              $direct="+";

diff --git a/readme.md b/readme.md
@@ -1,6 +1,6 @@
 # HLAminer
 
-## HLAminer v1.3.4 Rene L. Warren (c) 2011-2016 
+## HLAminer v1.3.1 Rene L. Warren (c) 2011-2017 
 ## email: rwarren [at] bcgsc [dot] ca
 ## Visit www.bcgsc.ca/bioinfo/software/hlaminer for additional information
 
@@ -37,9 +37,9 @@
 ### LICENSE <a name="LICENSE"></a>
 --------
 
-  HLAminer Copyright (c) 2011-2016 Canada's Michael Smith Genome Science Centre.  All rights reserved.
-  TASR Copyright   (c) 2010-2016 Canada's Michael Smith Genome Science Centre.  All rights reserved.
-  SSAKE Copyright  (c) 2006-2016 Canada's Michael Smith Genome Science Centre.  All rights reserved.
+  HLAminer Copyright (c) 2011-2017 Canada's Michael Smith Genome Science Centre.  All rights reserved.
+  TASR Copyright   (c) 2010-2017 Canada's Michael Smith Genome Science Centre.  All rights reserved.
+  SSAKE Copyright  (c) 2006-2017 Canada's Michael Smith Genome Science Centre.  All rights reserved.
 
   Due to the clinical implications of HLAminer, the code is now released
   under the BC Cancer Agency software license agreement (academic use).