From 8c1668faa4802004a95eb2ea4596608a943b528f Mon Sep 17 00:00:00 2001 From: Eric Coissac Date: Thu, 23 May 2024 17:46:00 +0200 Subject: [PATCH] patch some compile warnings --- src/ecoprimer.c | 4 ++++ src/libecoPCR/ecoseq.c | 2 +- src/libecoPCR/ecotax.c | 4 ++-- src/libecoprimer/apat_search.c | 4 ++-- src/libecoprimer/aproxpattern.c | 2 +- src/libecoprimer/libstki.c | 3 +-- src/libecoprimer/libstki.h | 2 ++ src/libecoprimer/merge.c | 4 ++-- 8 files changed, 15 insertions(+), 10 deletions(-) diff --git a/src/ecoprimer.c b/src/ecoprimer.c index d588256..d8a84ec 100644 --- a/src/ecoprimer.c +++ b/src/ecoprimer.c @@ -794,6 +794,10 @@ int main(int argc, char **argv) } } + + if (errflag) { + ExitUsage(1); + } options.pnparm = &nnparams; if (options.saltmethod != 2) //if not SALT_METHOD_OWCZARZY options.saltmethod = SALT_METHOD_SANTALUCIA; //then force SALT_METHOD_SANTALUCIA diff --git a/src/libecoPCR/ecoseq.c b/src/libecoPCR/ecoseq.c index 9483ade..18c943b 100644 --- a/src/libecoPCR/ecoseq.c +++ b/src/libecoPCR/ecoseq.c @@ -195,7 +195,7 @@ ecoseq_t *ecoseq_iterator(const char *prefix) { static FILE *current_seq_file= NULL; static int32_t current_file_idx = 1; - static char current_prefix[1024]; + static char current_prefix[1025]; ecoseq_t *seq; if (prefix) diff --git a/src/libecoPCR/ecotax.c b/src/libecoPCR/ecotax.c index 95b304e..2a39367 100644 --- a/src/libecoPCR/ecotax.c +++ b/src/libecoPCR/ecotax.c @@ -32,7 +32,7 @@ ecotxidx_t *read_taxonomyidx(const char *filename,const char *filename2) fprintf(stderr,"Reading %d taxa...\n",count); for (i=0; i < count; i++){ readnext_ecotaxon(f,&(index->taxon[i])); - index->taxon[i].parent=index->taxon + (int32_t)index->taxon[i].parent; + index->taxon[i].parent=index->taxon + (int64_t)index->taxon[i].parent; } if (count2>0) @@ -42,7 +42,7 @@ ecotxidx_t *read_taxonomyidx(const char *filename,const char *filename2) for (i=0; i < count2; i++){ readnext_ecotaxon(f2,&(index->taxon[count+i])); - index->taxon[count+i].parent=index->taxon + (int32_t)index->taxon[count+i].parent; + index->taxon[count+i].parent=index->taxon + (int64_t)index->taxon[count+i].parent; } return index; diff --git a/src/libecoprimer/apat_search.c b/src/libecoprimer/apat_search.c index fc42b7a..3da4070 100644 --- a/src/libecoprimer/apat_search.c +++ b/src/libecoprimer/apat_search.c @@ -39,7 +39,7 @@ int32_t ManberNoErr(pecoseq_t pseq,ppattern_t pat, u_int32_t pos; uint32_t smask, r; uint8_t *data; - int32_t end; + uint32_t end; end = (size_t)(pseq->SQ_length); @@ -88,7 +88,7 @@ int32_t ManberSub(pecoseq_t pseq,ppattern_t pat, uint32_t smask, cmask, sindx; uint32_t *pr, r[2 * MAX_PAT_ERR + 2]; uint8_t *data; - int32_t end; + uint32_t end; end = (size_t)(pseq->SQ_length); diff --git a/src/libecoprimer/aproxpattern.c b/src/libecoprimer/aproxpattern.c index 3433044..a374afd 100644 --- a/src/libecoprimer/aproxpattern.c +++ b/src/libecoprimer/aproxpattern.c @@ -59,7 +59,7 @@ void encodeSequence(ecoseq_t *seq) data = (uint8_t*)(seq->SQ); cseq = seq->SQ; - for (i=0;iSQ_length;i++,data++,cseq++) + for (i=0;i<(int)(seq->SQ_length);i++,data++,cseq++) { *data = encoder[(IS_UPPER(*cseq) ? *cseq : 'Z') - 'A']; } diff --git a/src/libecoprimer/libstki.c b/src/libecoprimer/libstki.c index 9bdebf2..024aa23 100644 --- a/src/libecoprimer/libstki.c +++ b/src/libecoprimer/libstki.c @@ -250,8 +250,7 @@ void CursiToTop(StackiPtr stki) } /* end of CursiToTop */ -void CursiToBottom(stki) - StackiPtr stki; +void CursiToBottom(StackiPtr stki) { stki->cursor = 0; diff --git a/src/libecoprimer/libstki.h b/src/libecoprimer/libstki.h index cad7d60..30b30fb 100644 --- a/src/libecoprimer/libstki.h +++ b/src/libecoprimer/libstki.h @@ -16,6 +16,7 @@ #include "ecotype.h" +#include /* ==================================================== */ /* Constantes de dimensionnement */ @@ -85,5 +86,6 @@ bool_t SearchDownStacki (StackiPtr stki , int32_t sval ); bool_t BinSearchStacki (StackiPtr stki , int32_t sval ); bool_t SameStacki (StackiPtr stki1 , StackiPtr stki2 ); bool_t ReverseStacki (StackiPtr stki ); +void CursiToBottom (StackiPtr stki ); #endif /* _H_libstki */ diff --git a/src/libecoprimer/merge.c b/src/libecoprimer/merge.c index c27b6cb..1b16730 100644 --- a/src/libecoprimer/merge.c +++ b/src/libecoprimer/merge.c @@ -41,7 +41,7 @@ void ecomerge(pwordcount_t data,uint32_t s1,uint32_t s2,uint32_t remainingSeq,ui uint32_t currentcount,tmpcount; int same; queue_t queue; - int nsame=0; + // int nsame=0; uint32_t maxcount=0; bool_t writed=TRUE; @@ -103,7 +103,7 @@ void ecomerge(pwordcount_t data,uint32_t s1,uint32_t s2,uint32_t remainingSeq,ui * record if the two words in the both subtable are the same */ same = (source != S2) && (WORD(currentword) == WORD(merged.words[merged.read2])); - nsame+=same; + // nsame+=same; // DEBUG_LOG("Merging : r1 = %d s1 = %d r2 = %d size = %d word = %s source=%u same=%u",merged.read1,s1,merged.read2-s1,merged.size,ecoUnhashWord(currentword,18),source,same)