--no commit message

python/orgasm-1.py

@@ -5,11 +5,17 @@
 # ./orgasm/build/lib.macosx-10.6-intel-2.7/
 # python orgasm-1.py GWM-261 COX1.fasta
 
-from orgasm.tango import tango, matchtoseed, cutLowCoverage, scaffold, coverageEstimate
+from orgasm.tango import tango, \
+                         matchtoseed, \
+                         cutLowCoverage, \
+                         scaffold, \
+                         coverageEstimate, \
+                         insertFragment
 from orgasm.indexer import _orgasm as indexer
 from orgasm.backtranslate.fasta import fasta
 from orgasm.assembler import Assembler
-
+from orgasm.multialign import multiAlignReads, \
+                              consensus
 import sys
 
 if __name__ == '__main__':

python/orgasm/version.py

+major = 0
+minor = 0
+serial= 'alpha'
+
+version = "%2d.%02d %s" % (major,minor,serial)

src/buildcode.c

@@ -14,7 +14,7 @@ int main(int argc, char *argv[])
 	uint32_t icode;
 	char     nuc[9];
 	int i;
-	uint16_t mask;
+//	uint16_t mask;
 
 	nuc[8]=0;
 

src/buildcomplement.c

@@ -18,7 +18,7 @@ int main(int argc, char *argv[])
 	char     cnuc[5];
 
 	int i;
-	uint16_t mask;
+//	uint16_t mask;
 
 	nuc[4]=0;
 	cnuc[4]=0;

src/buildindex.c

@@ -21,7 +21,7 @@ buffer_t *buildIndex(const char *forwardFileName, const char* reverseFileName,
 	char* indexFileName;
 
 //	uint32_t indexcount;
-	uint32_t i;
+//	uint32_t i;
 	buffer_t *reads;
 
 	forward = fopen(forwardFileName,"r");

src/compsort.c

@@ -38,14 +38,14 @@ void partialCompSortBuffer(buffer_t *buffer,
 	uint8_t  word;
 	uint32_t i;
 	uint32_t swap;
-	uint32_t pairswap;
+//	uint32_t pairswap;
 	uint32_t next;
 	uint32_t first;
-	uint32_t pair;
-	uint32_t *pairp;
+//	uint32_t pair;
+//	uint32_t *pairp;
 	uint32_t *swapp;
 	uint32_t cumsum=start;
-	uint32_t backtolastswap=FALSE;
+//	uint32_t backtolastswap=FALSE;
 	int32_t shiftmax=0;
 
 	if (shift > shiftmax) shiftmax=shift;

src/decode.c

@@ -34,13 +34,13 @@ char * decode(buffer_t *buffer, uint32_t recordid, uint32_t begin, int32_t lengt
 	uint32_t    shift;
 	uint32_t    i;
 	uint32_t    lcompact;
-	uint32_t    mask;
+//	uint32_t    mask;
 	uint16_t    *compactseq;
 
 	if (dest==NULL) dest = internal;
 
 	dest = (char*)PTR8(dest);
-	idest = (uint16_t*)dest;
+	idest = (uint64_t*)dest;
 
 	from = recordid * buffer->recordSize + ((begin >> 2) & 0xFFFFFFFE);
 	shift = begin & 7;
@@ -66,7 +66,7 @@ char *decodeComp(buffer_t *buffer, uint32_t recordid, uint32_t begin, int32_t le
 	uint32_t    shift;
 	int32_t     i;
 	uint32_t    lcompact;
-	uint32_t    mask;
+//	uint32_t    mask;
 	uint16_t    *compactseq;
 	size_t      lkey;
 	char*       key;
@@ -76,7 +76,7 @@ char *decodeComp(buffer_t *buffer, uint32_t recordid, uint32_t begin, int32_t le
 
 	dest = (char*)PTR8(dest);
 	dest2 = (char*)PTR8(internal2);
-	idest = (uint16_t*)dest;
+	idest = (uint64_t*)dest;
 
 	from = buffer->readSize - begin;
 
@@ -103,7 +103,7 @@ char *decodeComp(buffer_t *buffer, uint32_t recordid, uint32_t begin, int32_t le
 	shift = (4 - (from & 3)) & 3;
 
 
-    ASSERT (shift <4,"There is a bug readsize = %d begin = %d shift=%d",buffer->readSize,begin,shift)
+    ASSERT (shift <4,"There is a bug readsize = %zu begin = %d shift=%d",buffer->readSize,begin,shift)
 
 	lcompact = (length+shift) / 8 + (((length+shift) & 7) ? 1:0);
 
@@ -149,13 +149,13 @@ char * decodeSequence(pnuc buffer, uint32_t begin, int32_t length, char *dest)
 	uint32_t    shift;
 	uint32_t    i;
 	uint32_t    lcompact;
-	uint32_t    mask;
+//	uint32_t    mask;
 	uint16_t    *compactseq;
 
 	if (dest==NULL) dest = internal;
 
 	dest = (char*)PTR8(dest);
-	idest = (uint16_t*)dest;
+	idest = (uint64_t*)dest;
 
 	from = ((begin >> 2) & 0xFFFFFFFE);
 	shift = begin & 7;

src/fastq.c

@@ -204,7 +204,7 @@ buffer_t * loadPairedFastq(FILE* forward,
 	char*    bufferend;
 //	uint32_t readLength;
 	uint32_t recordLength;
-	uint32_t nextprint;
+	uint32_t nextprint=0;
 	uint32_t* encodedseqs;
 	buffer_t* seqbuffer;
 
@@ -227,7 +227,7 @@ buffer_t * loadPairedFastq(FILE* forward,
 	seqbuffer  = newBuffer(maxbuffersize,readLength,maxread);
 	encodedseqs= (uint32_t*)(seqbuffer->records);
 
-	printf("maximum reads : %d\n",seqbuffer->maxrecord);
+	printf("maximum reads : %zu\n",seqbuffer->maxrecord);
 
 
 	while (readLength && (seqbuffer->readCount+2) <= seqbuffer->maxrecord)

src/load.c

@@ -14,7 +14,7 @@ void indexReverseComplement(buffer_t *reads)
 	if (reads->complement)
 		FREE(reads->complement);
 
-	reads->complement=(int32_t*) MALLOC(sizeof(int32_t) * reads->readCount);
+	reads->complement=(uint32_t*) MALLOC(sizeof(uint32_t) * reads->readCount);
 
 	for (i=0;i < reads->readCount; i++)
 		reads->complement[reads->order1[i]]=i;

src/lookfor.c

@@ -249,7 +249,7 @@ int32_t lookForForward(buffer_t *buffer, pnuc key, size_t length, int32_t* endof
 	int32_t end;
 	int32_t middle;
 	int32_t comp;
-	int32_t comp1;
+//	int32_t comp1;
 
 	// I set the end of list flag to 0
 	*endoflist=0;
@@ -436,7 +436,7 @@ int32_t lookForReverse(buffer_t *buffer, pnuc key, size_t length, int32_t* endof
 int32_t nextReverse(buffer_t *buffer, int32_t current, size_t length, int32_t* endoflist)
 {
 	int32_t pos= current+1;
-	int32_t lkey = CODELENGTH(buffer->readSize);
+//	int32_t lkey = CODELENGTH(buffer->readSize);
 	pnuc    key= (pnuc)((uint8_t*)(buffer->records) + buffer->recordSize * buffer->order1[current]);
 	int32_t rshift= buffer->readSize & 3;
 	int     comp=cmpCompPrefix(buffer,buffer->order1[pos],key, length + ((rshift==0) ? 0:(4-rshift)));

src/orgasm.h

@@ -132,6 +132,8 @@ void writeGeneralData(buffer_t *buffer,FILE* output);
 void loadSequences(buffer_t *buffer,FILE* input);
 void loadPairData(buffer_t *buffer,FILE* input);
 void loadGeneralData(buffer_t *buffer,FILE* input);
+uint32_t loadOrder1(buffer_t *buffer,FILE* input);
+
 
 void fillOrdored(buffer_t *buffer);
 void sortBuffer(buffer_t *buffer);
@@ -162,5 +164,9 @@ extern uint32_t expanded8bitsnuc[];
 pnuc encodeSequence(pnuc dest, char* src, uint32_t length);
 pnuc shiftKey(pnuc dest, pnuc key,uint32_t shift, uint32_t keyLength);
 
+void countLetterAt(buffer_t *buffer,uint32_t pos);
+uint32_t minSuffix(buffer_t *buffer,uint32_t pos);
+
+
 
 #endif /* ORGASM_H_ */

src/orgasmi.c

@@ -143,7 +143,11 @@ if ((argc -= optind) == 2)
 	strcpy(reverseFileName,argv[optind]);
 }
 else
+{
 	errflag++;
+	forwardFileName=NULL;
+	reverseFileName=NULL;
+}
 
 
 if (indexfiles == NULL)