lots of PSL related changes

[biopieces.git] / code_perl / Maasha / UCSC / PSL.pm

diff --git a/code_perl/Maasha/UCSC/PSL.pm b/code_perl/Maasha/UCSC/PSL.pm
index 4c645658313e4bd963a8301c52d789a3fd9dcad0..a45006ec0bfbb85967cf31d33bb38b1ac71c16df 100644 (file)
--- a/code_perl/Maasha/UCSC/PSL.pm
+++ b/code_perl/Maasha/UCSC/PSL.pm
@@ -84,8 +84,8 @@ use constant {
     S_LEN       => 14,
     S_BEG       => 15,
     S_END       => 16,
-    BLOCKCOUNT  => 17,
-    BLOCKSIZES  => 18,
+    BLOCK_COUNT => 17,
+    BLOCK_LENS  => 18,
     Q_BEGS      => 19,
     S_BEGS      => 20,
 };
@@ -134,28 +134,28 @@ sub psl2record
     my %record;
 
     %record = (
-        REC_TYPE    => "PSL",
-        BLOCKSIZES  => $psl->{ 'blockSize' },
-        SNUMINSERT  => $psl->{ 'tNumInsert' },
-        Q_END       => $psl->{ 'qEnd' },
-        SBASEINSERT => $psl->{ 'tBaseInsert' },
-        S_END       => $psl->{ 'tEnd' },
-        QBASEINSERT => $psl->{ 'qBaseInsert' },
-        REPMATCHES  => $psl->{ 'repMatches' },
-        QNUMINSERT  => $psl->{ 'qNumInsert' },
-        MISMATCHES  => $psl->{ 'misMatches' },
-        BLOCKCOUNT  => $psl->{ 'blockCount' },
-        Q_LEN       => $psl->{ 'qSize' },
-        S_ID        => $psl->{ 'tName' },
-        STRAND      => $psl->{ 'strand' },
-        Q_ID        => $psl->{ 'qName' },
-        MATCHES     => $psl->{ 'matches' },
-        S_LEN       => $psl->{ 'tSize' },
-        NCOUNT      => $psl->{ 'nCount' },
-        Q_BEGS      => $psl->{ 'qStarts' },
-        S_BEGS      => $psl->{ 'tStarts' },
-        S_BEG       => $psl->{ 'tStart' },
-        Q_BEG       => $psl->{ 'qStart ' },
+        REC_TYPE     => "PSL",
+        BLOCK_LENS   => $psl->{ 'blockSize' },
+        SNUMINSERT   => $psl->{ 'tNumInsert' },
+        Q_END        => $psl->{ 'qEnd' },
+        SBASEINSERT  => $psl->{ 'tBaseInsert' },
+        S_END        => $psl->{ 'tEnd' },
+        QBASEINSERT  => $psl->{ 'qBaseInsert' },
+        REPMATCHES   => $psl->{ 'repMatches' },
+        QNUMINSERT   => $psl->{ 'qNumInsert' },
+        MISMATCHES   => $psl->{ 'misMatches' },
+        BLOCK_COUNT  => $psl->{ 'blockCount' },
+        Q_LEN        => $psl->{ 'qSize' },
+        S_ID         => $psl->{ 'tName' },
+        STRAND       => $psl->{ 'strand' },
+        Q_ID         => $psl->{ 'qName' },
+        MATCHES      => $psl->{ 'matches' },
+        S_LEN        => $psl->{ 'tSize' },
+        NCOUNT       => $psl->{ 'nCount' },
+        Q_BEGS       => $psl->{ 'qStarts' },
+        S_BEGS       => $psl->{ 'tStarts' },
+        S_BEG        => $psl->{ 'tStart' },
+        Q_BEG        => $psl->{ 'qStart ' },
     );
 
     $record{ "SCORE" } = $record{ "MATCHES" } + int( $record{ "REPMATCHES" } / 2 ) - $record{ "MISMATCHES" } - $record{ "QNUMINSERT" } - $record{ "SNUMINSERT" };