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Added the possibility to use standard input as input for sequence

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This commit is contained in:
Celine Mercier
2016-02-22 15:29:22 +01:00
parent 0c4c37d5ab
commit d44eca19ce
1 changed files with 7 additions and 3 deletions
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10
libfasta/sequence.c
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@ -223,7 +223,13 @@ fastaSeqCount seq_readAllSeq2(char *fileName, BOOL isStandardSeq, BOOL onlyATGC)
fastaSeqCount allseqs; fastaSeqCount allseqs;
int32_t discarded=0; int32_t discarded=0;
fp = file_open(fileName, TRUE); if ((fileName == NULL) || (strcmp(fileName, "-") == 0))
fp = stdin;
else
{
fp = file_open(fileName, TRUE);
exitIfEmptyFile(fp);
}
if (fp == NULL) if (fp == NULL)
{ {
@ -231,8 +237,6 @@ fastaSeqCount seq_readAllSeq2(char *fileName, BOOL isStandardSeq, BOOL onlyATGC)
exit(1); exit(1);
} }
exitIfEmptyFile(fp);
seqPtrAr = (fastaSeqPtr) util_malloc(slots*sizeof(fastaSeq), __FILE__, __LINE__); seqPtrAr = (fastaSeqPtr) util_malloc(slots*sizeof(fastaSeq), __FILE__, __LINE__);
seqPtr = seq_getNext(fp, " ", isStandardSeq, onlyATGC); seqPtr = seq_getNext(fp, " ", isStandardSeq, onlyATGC);