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/*===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
*/
/*
lex file is three sections:
definitions: name definition
%%
rules: pattern action
%%
user code
*/
/*
@HD\tVN:1.4\tSO:coordinate
@SQ\tSN:1\t...
@SQ\tSN:16\t...
@RG\tID:PM89\tPL:Illumina\tLB...
HWI-...
*/
%top{
#include <stdio.h>
#include <unistd.h>
#include <string.h>
#include "sam.tab.h"
//#define YYSTYPE char
#define LEXDEBUG 0
// do { if (LEXDEBUG) fprintf(stderr, "%s:%d:%s(): " fmt, __FILE__, __LINE__, __func__, __VA_ARGS__); } while (0)
#define lex_print(fmt, ...) \
do { if (LEXDEBUG) fprintf(stderr, fmt, ##__VA_ARGS__); } while (0)
}
/* definitions */
digits [[:digit:]]+
integer [-+]?[0-9]+
float [-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?
eol (\r\n|\r|\n)
controlchar [\x00-\x08\x0b-\x0c\x0e-\x1f]
tag [A-Za-z][A-Za-z0-9]
/* validtag VN|SO|GO|SN|LN|AS|M5|SP|UR|ID|CN|DS|DT|FO|KS|LB|PG|PI|PL|PM|PU|SM|ID|PN|CL|PP|DS|VN */
attv {tag}:A:[!-~]
ittv {tag}:i:{integer}
fttv {tag}:f:{float}
zttv {tag}:Z:[[:print:]]*
httv {tag}:H:([0-9A-F][0-9A-F])*
bttv {tag}:B:[cCsSiIf](,{float})+
ttv {attv}|{ittv}|{fttv}|{zttv}|{httv}|{bttv}
/* No @ in first, to distinguish from headers */
qname [!-?A-~][!-~]{0,253}
/* stop after first EOF */
%option noyywrap
%option prefix="SAM"
%option warn
%option nodefault
%option nodebug
/* Not a TTY */
%option never-interactive
%option yylineno
%option nounistd
/* Allow multitheading */
/* %option reentrant */
/* yylex takes yylval */
/* %option bison-bridge */
%x INALIGNMENT
%x AFTERCOLON
%%
/* rules */
/* TODO: lots of strdups, when do we free()? */
^@HD { lex_print( "lex: Header\n"); return HEADER; }
^@SQ { lex_print( "lex: SQ\n"); return SEQUENCE; }
^@RG { lex_print( "lex: RG\n"); return READGROUP; }
^@PG { lex_print( "lex: PG\n"); return PROGRAM; }
^@CO\t.*{eol} { lex_print( "lex: Comment\n"); return COMMENT; }
<INITIAL,INALIGNMENT>^{qname} { BEGIN INALIGNMENT; SAMlval.strval=strdup(yytext); lex_print("\nlex: alignment qname, INALIGNMENT\n"); return QNAME; }
<INITIAL,INALIGNMENT,AFTERCOLON>{controlchar} { lex_print("lex:CONTROLCHAR1\n"); return CONTROLCHAR; }
<INITIAL,INALIGNMENT>\t { lex_print("lex: tab\n"); return TAB;}
<AFTERCOLON>\t { BEGIN INITIAL; lex_print("lex: tab INITIAL\n"); return TAB;}
<INITIAL,INALIGNMENT,AFTERCOLON>{eol} { BEGIN INITIAL; lex_print("lex: eol INITIAL\n"); return EOL;}
/* <INALIGNMENT>{ttv} { lex_print("lex: ttv\n"); return TTV; } */
<INALIGNMENT>[ -~]+ { SAMlval.strval=strdup(yytext); lex_print("lex: alignvalue\n"); return ALIGNVALUE; }
{tag} { SAMlval.strval=strdup(yytext); lex_print("lex: Valid Tag:%s\n", yytext); return TAG; }
<INITIAL,INALIGNMENT>: { BEGIN AFTERCOLON; lex_print("lex: colon AFTERCOLON\n"); return COLON;}
<AFTERCOLON>[ -~]+ { SAMlval.strval=strdup(yytext); lex_print("lex: Value:%s\n", yytext); return VALUE; }
/* \t[!-~]+ { lex_print("lex: alignment field\n"); return ALIGNMENT; }
\t{ttv} { lex_print("lex: optional alignment\n"); return ALIGNMENT; }
*/
/*
\t{flag} { lex_print("lex: alignment flag\n"); return ALIGNMENT; }
\t{mapq} { lex_print("lex: alignment mapq\n"); return ALIGNMENT; }
\t{cigar} { lex_print("lex: alignment cigar\n"); return ALIGNMENT; }
\t{rnext} { lex_print("lex: alignment rnext\n"); return ALIGNMENT; }
\t{pnext} { lex_print("lex: alignment pnext\n"); return ALIGNMENT; }
\t{tlen} { lex_print("lex: alignment tlen\n"); return ALIGNMENT; }
\t{seq} { lex_print("lex: alignment seq\n"); return ALIGNMENT; }
\t{qual} { lex_print("lex: alignment qual\n"); return ALIGNMENT; }
\t{ttv} { lex_print("lex: alignment ttv\n"); return ALIGNMENT; }
\t{rname} { lex_print("lex: alignment rname\n"); return ALIGNMENT; }
\t{pos} { lex_print("lex: alignment pos\n"); return ALIGNMENT; }
*/
/*
^@VN\t{version}\n printf("lex: Version\n");
^{hdrtag}(\t[[:alpha:]][[:alnum:]]:[[:print:]]+)+\n printf("lex: Allowed Header %d %s", yyleng, yytext);
^@[[:upper:]]{2}(\t[[:alpha:]][[:alnum:]]:[[:print:]]+)+\n printf("lex: Header %d %s", yyleng, yytext);
^@[[:upper:]]{2}(\t[[:alpha:]][[:alnum:]]+:[[:print:]]+)+\n printf("lex: Header long %d %s", yyleng, yytext);
^{qname}\t{flag}\t{rname}\t{pos}\t{mapq}\t{cigar}\t{rnext}\t{pnext}\t{tlen}\t{seq}\t{qual}\n printf("lex: Alignment\n");
^{qname}\t{flag}\t{rname}\t{pos}\t{mapq}\t{cigar}\t{rnext}\t{pnext}\t{tlen}\t{seq}\t{qual}({ttv})+\n {
char * s1=strdup(yytext);
printf("lex: Alignment with optional: %s\n", s1);
char * s2=s1;
char * tok;
while ((tok=strsep(&s2,"\t")))
{
printf(" Token:%s\n", tok);
}
free(s1);
}
^@[[:lower:]]{2}\t.*\n printf("Optional, lowercase tag\n");
^@HD.*\n printf("Empty HD: %s %d", yytext, yyleng);
^[^@].*\n printf("not at: %s", yytext);
*/
.|\n lex_print("DEFAULT '%c' ", *yytext);
%%
/* user code */
/*
int main(int argc, char * argv[])
{
SAMlex();
// SAMparse();
}
*/
|
