remove trailing whitespace

diff --git a/magic/Magdir/bioinformatics b/magic/Magdir/bioinformatics
index 7de08a1e0088a2901869ef1a225552f83b4a8536..07d92a617afb7009ccd42c50bcafc322f34b19bf 100644 (file)
--- a/magic/Magdir/bioinformatics
+++ b/magic/Magdir/bioinformatics
@@ -1,6 +1,6 @@
 
 #------------------------------------------------------------------------------
-# $File: bioinformatics,v 1.2 2016/02/14 15:53:53 christos Exp $
+# $File: bioinformatics,v 1.3 2016/06/20 16:13:14 christos Exp $
 # bioinfomatics:  file(1) magic for Bioinfomatics file formats
 
 ###############################################################################
@@ -16,32 +16,32 @@
 
 
 ###############################################################################
-# Tabix index file 
+# Tabix index file
 # used by SAMtools bgzip/tabix (http://samtools.sourceforge.net/tabix.shtml)
 ###############################################################################
 0      string  TBI\1           SAMtools TBI (Tabix index format)
 >0x04  lelong  =1              \b, with %d reference sequence
 >0x04  lelong  >1              \b, with %d reference sequences
 >0x08  lelong  &0x10000        \b, using half-closed-half-open coordinates (BED style)
->0x08  lelong  ^0x10000        
+>0x08  lelong  ^0x10000
 >>0x08 lelong  =0              \b, using closed and one based coordinates (GFF style)
 >>0x08 lelong  =1              \b, using SAM format
 >>0x08 lelong  =2              \b, using VCF format
 >0x0c  lelong  x               \b, sequence name column: %d
 >0x10  lelong  x               \b, region start column: %d
->0x08  lelong  =0              
+>0x08  lelong  =0
 >>0x14 lelong  x               \b, region end column: %d
 >0x18  byte    x               \b, comment character: %c
 >0x1c  lelong  x               \b, skip line count: %d
 
 
 ###############################################################################
-# BAM (Binary Sequence Alignment/Map format) 
-# used by SAMtools (http://samtools.sourceforge.net/SAM1.pdf) 
+# BAM (Binary Sequence Alignment/Map format)
+# used by SAMtools (http://samtools.sourceforge.net/SAM1.pdf)
 # data is normally present only within compressed BGZF blocks (CDATA), so use file -z to examine it
 ###############################################################################
 0      string  BAM\1   SAMtools BAM (Binary Sequence Alignment/Map)
->0x04  lelong  >0      
+>0x04  lelong  >0
 >>&0x00 regex  =^[@]HD\t.*VN:          \b, with SAM header
 >>>&0  regex   =[0-9.]+                \b version %s
 >>&(0x04)      lelong  >0      \b, with %d reference sequences
@@ -49,14 +49,14 @@
 
 ###############################################################################
 # BAI (BAM indexing format)
-# used by SAMtools (http://samtools.sourceforge.net/SAM1.pdf) 
+# used by SAMtools (http://samtools.sourceforge.net/SAM1.pdf)
 ###############################################################################
 0              string  BAI\1   SAMtools BAI (BAM indexing format)
 >0x04          lelong  >0      \b, with %d reference sequences
 
 
 ###############################################################################
-# CRAM (Binary Sequence Alignment/Map format) 
+# CRAM (Binary Sequence Alignment/Map format)
 ###############################################################################
 0      string  CRAM    CRAM
 >0x04  byte    >-1     version %d.
@@ -69,13 +69,13 @@
 # used by SAMtools & VCFtools (http://vcftools.sourceforge.net/bcf.pdf)
 # data is normally present only within compressed BGZF blocks (CDATA), so use file -z to examine it
 ###############################################################################
-0              string     BCF\4    
+0              string     BCF\4
 # length of seqnm data in bytes is positive
->&0x00         lelong    >0    
+>&0x00         lelong    >0
 # length of smpl data in bytes is positive
 >>&(&-0x04)    lelong    >0                    SAMtools BCF (Binary Call Format)
 # length of meta in bytes
->>>&(&-0x04)   lelong    >0    
+>>>&(&-0x04)   lelong    >0
 # have meta text string
 >>>>&0x00      search    ##samtoolsVersion=
 >>>>>&0x00     string    x                     \b, generated by SAMtools version %s
@@ -88,7 +88,7 @@
 ###############################################################################
 0              string     BCF\2\1    Binary Call Format (BCF) version 2.1
 # length of header text
->&0x00         lelong    >0    
+>&0x00         lelong    >0
 # have header string
 >>&0x00 search   ##samtoolsVersion=
 >>>&0x00       string    x                     \b, generated by SAMtools version %s
@@ -101,7 +101,7 @@
 ###############################################################################
 0              string     BCF\2\2    Binary Call Format (BCF) version 2.2
 # length of header text
->&0x00         lelong    >0    
+>&0x00         lelong    >0
 # have header string
 >>&0x00 search   ##samtoolsVersion=
 >>>&0x00       string    x                     \b, generated by SAMtools version %s
@@ -119,11 +119,11 @@
 ###############################################################################
 # XXX Broken?
 # @<seqname>
-#0     regex   =^@[A-Za-z0-9_.:-]+\?\n 
+#0     regex   =^@[A-Za-z0-9_.:-]+\?\n
 # <seq>
 #>&1   regex   =^[A-Za-z\n.~]++
 # +[<seqname>]
-#>>&1  regex   =^[A-Za-z0-9_.:-]*\?\n  
+#>>&1  regex   =^[A-Za-z0-9_.:-]*\?\n
 # <qual>
 #>>>&1 regex   =^[!-~\n]+\n            FASTQ
 
@@ -132,7 +132,7 @@
 # used by FASTA (http://fasta.bioch.virginia.edu/fasta_www2/fasta_guide.pdf)
 ###############################################################################
 #0     byte    0x3e
-# q>0  regex   =^[>][!-~\t\ ]+$        
+# q>0  regex   =^[>][!-~\t\ ]+$
 # Amino Acid codes: [A-IK-Z*-]+
 #>>1   regex   !=[!-'Jj;:=?@^`|~\\]            FASTA
 # IUPAC codes/gaps: [ACGTURYKMSWBDHVNX-]+
@@ -141,37 +141,37 @@
 #>>>1  regex   =^[EFIJLOPQZefijlopqz]+$        \b, with Amino Acid codes
 
 ###############################################################################
-# SAM (Sequence Alignment/Map format) 
-# used by SAMtools (http://samtools.sourceforge.net/SAM1.pdf) 
+# SAM (Sequence Alignment/Map format)
+# used by SAMtools (http://samtools.sourceforge.net/SAM1.pdf)
 ###############################################################################
 # Short-cut version to recognise SAM files with (optional) header at beginning
 ###############################################################################
-0      string     @HD\t        
+0      string     @HD\t
 >4     search     VN:          Sequence Alignment/Map (SAM), with header
 >>&0   regex      [0-9.]+      \b version %s
 ###############################################################################
 # Longer version to recognise SAM alignment lines using (many) regexes
 ###############################################################################
 # SAM Alignment QNAME
-0              regex   =^[!-?A-~]{1,255}(\t[^\t]+){11}         
+0              regex   =^[!-?A-~]{1,255}(\t[^\t]+){11}
 # SAM Alignment FLAG
->0             regex   =^([^\t]+\t){1}[0-9]{1,5}\t             
+>0             regex   =^([^\t]+\t){1}[0-9]{1,5}\t
 # SAM Alignment RNAME
->>0            regex   =^([^\t]+\t){2}\\*|[^*=]*\t             
+>>0            regex   =^([^\t]+\t){2}\\*|[^*=]*\t
 # SAM Alignment POS
->>>0           regex   =^([^\t]+\t){3}[0-9]{1,9}\t             
+>>>0           regex   =^([^\t]+\t){3}[0-9]{1,9}\t
 # SAM Alignment MAPQ
->>>>0          regex   =^([^\t]+\t){4}[0-9]{1,3}\t             
+>>>>0          regex   =^([^\t]+\t){4}[0-9]{1,3}\t
 # SAM Alignment CIGAR
->>>>>0         regex   =\t\\*|([0-9]+[MIDNSHPX=])+)\t          
+>>>>>0         regex   =\t\\*|([0-9]+[MIDNSHPX=])+)\t
 # SAM Alignment RNEXT
->>>>>>0                regex   =\t(\\*|=|[!-()+->?-~][!-~]*)\t         
+>>>>>>0                regex   =\t(\\*|=|[!-()+->?-~][!-~]*)\t
 # SAM Alignment PNEXT
->>>>>>>0       regex   =^([^\t]+\t){7}[0-9]{1,9}\t             
+>>>>>>>0       regex   =^([^\t]+\t){7}[0-9]{1,9}\t
 # SAM Alignment TLEN
->>>>>>>>0      regex   =\t[+-]{0,1}[0-9]{1,9}\t.*\t            
+>>>>>>>>0      regex   =\t[+-]{0,1}[0-9]{1,9}\t.*\t
 # SAM Alignment SEQ
->>>>>>>>>0     regex   =^([^\t]+\t){9}(\\*|[A-Za-z=.]+)\t      
+>>>>>>>>>0     regex   =^([^\t]+\t){9}(\\*|[A-Za-z=.]+)\t
 # SAM Alignment QUAL
 >>>>>>>>>>0    regex   =^([^\t]+\t){10}[!-~]+  Sequence Alignment/Map (SAM)
 >>>>>>>>>>>0   regex   =^[@]HD\t.*VN:          \b, with header