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Accept to deal with sequence in lower case

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git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@217 60f365c0-8329-0410-b2a4-ec073aeeaa1d
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Eric Coissac
2009-05-13 13:21:10 +00:00
parent 1428cd7499
commit ad6f493d0f
9 changed files with 261 additions and 42 deletions
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.cproject
+122
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.project
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<?xml version="1.0" encoding="UTF-8"?>
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<comment></comment>
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.pydevproject
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<?xml version="1.0" encoding="UTF-8"?>
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<pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 2.4</pydev_property>
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src/ecoPCR.gz
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src/ecofind.gz
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src/ecogrep
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src/ecoisundertaxon
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src/libecoPCR/ecoseq.c
+7
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@@ -4,6 +4,7 @@
#include <zlib.h> #include <zlib.h>
#include <string.h> #include <string.h>
#include <stdio.h> #include <stdio.h>
#include <ctype.h>
static FILE *open_seqfile(const char *prefix,int32_t index); static FILE *open_seqfile(const char *prefix,int32_t index);
@@ -97,6 +98,8 @@ ecoseq_t *readnext_ecoseq(FILE *f)
int32_t comp_status; int32_t comp_status;
unsigned long int seqlength; unsigned long int seqlength;
int32_t rs; int32_t rs;
char *c;
int32_t i;
raw = read_ecorecord(f,&rs); raw = read_ecorecord(f,&rs);
@@ -139,6 +142,10 @@ ecoseq_t *readnext_ecoseq(FILE *f)
if (comp_status != Z_OK) if (comp_status != Z_OK)
ECOERROR(ECO_IO_ERROR,"I cannot uncompress sequence data"); ECOERROR(ECO_IO_ERROR,"I cannot uncompress sequence data");
for (c=seq->SQ,i=0;i<seqlength;c++,i++)
*c=toupper(*c);
return seq; return seq;
} }