Technically works as 6.2.1.

sift (6.2.1-1) unstable; urgency=medium

  * Team upload.

  * New upstream version.

 -- Steffen Moeller <moeller@debian.org>  Thu, 12 Jul 2018 12:54:01 +0200

sift (4.0.3b-7) UNRELEASED; urgency=medium

  * d/u/metadata:

 FHCRC NONCOMMERCIAL LICENSE license.  The license does not restrict

 auto-building of the package.   Distribution on a royalty-free basis

 is allowed, therefore Debian is allowed to distribute the program.

Files-Excluded: bin/choose_seqs_via_psiblastseedmedian

                bin/clump_output_alignedseq

                bin/consensus_to_seq

                bin/fastaseqs

                bin/info_on_seqs

                bin/process_alignment

                bin/psiblast_res_to_fasta_dbpairwise

                bin/seqs_from_psiblast_res

		blimps/obj/*.o

Files: *

Copyright: 1993-2008, Fred Hutchinson Cancer Research Center

README

README_4.0.3

#README

#README_4.0.3

INSTALL

VERSION_UPDATE

Description: Fix gcc warnings.

Author: Michael Bienia <geser@ubuntu.com>

--- a/src/Alignment.c

+++ b/src/Alignment.c

@@ -766,7 +766,7 @@

Index: sift/src/Alignment.c

===================================================================

--- sift.orig/src/Alignment.c

+++ sift/src/Alignment.c

@@ -766,7 +766,7 @@ read_psiblast_header_until_first (FILE*

 void

 read_psiblast_header_until_first_alignment (FILE* fp)

 {

 	read_psiblast_header_until_first (fp);

@@ -783,7 +783,7 @@

@@ -783,7 +783,7 @@ read_psiblast_header_until_first_alignme

 int 

 read_psiblast_header_until_first_no_error (FILE* fp,int return_error )

 {

         while (!feof (fp) && fgets (line, LINE_LEN, fp) != NULL &&

                 strstr (line, "Sequences producing significant alignments") == NULL)

@@ -1694,7 +1694,7 @@

 	assert (fp != NULL);

 	fgets (line, LARGE_BUFF_LENGTH, fp);

 	if (strstr (line, "Query") == NULL) {

-		fprintf (stderr,"%s line should have Query:\n");

+		fprintf (stderr,"'%s' line should have 'Query'\n", line);

 		exit (-1);

 	}

 	strptr = strtok (line, " \t\r\n"); /* this should be Query */

--- a/src/PN_convert.c

+++ b/src/PN_convert.c

@@ -2184,7 +2184,7 @@

Index: sift/src/PN_convert.c

===================================================================

--- sift.orig/src/PN_convert.c

+++ sift/src/PN_convert.c

@@ -2032,7 +2032,7 @@ void init_frq_qij()

    else

    {

       fprintf (stderr, "Can't open file '%s': %s.\n", qijname, strerror(errno) );

       system( "pwd" );

       exit (-1);

    }

--- a/src/Psiblast.c

+++ b/src/Psiblast.c

@@ -77,14 +77,14 @@

 	buff = strstr(Buffer, "Score=");

         if (buff != NULL) {

-                sscanf (buff, "Score = %d", alignment->score);

+                sscanf (buff, "Score = %d", &alignment->score);

         } else {

                 fprintf (errorfp, "Unable to read Score, parsing incorrect");

                 exit (-1);

         }

         buff = strstr (Buffer, "Expect = ");

         if (buff != NULL) {

-                sscanf (buff, "Expect = %lf", alignment->evalue);

+                sscanf (buff, "Expect = %lf", &alignment->evalue);

         } else {

                 fprintf (errorfp, "Unable to read e-value, parsing incorrect");

                 exit (-1);

@@ -95,7 +95,7 @@

         fgets (Buffer, LARGE_BUFF_LENGTH, fp); /* get blank line */

         fgets (Buffer, LARGE_BUFF_LENGTH, fp); /* get first line */;

         get_start_pos = TRUE;

-        while (Buffer != "\n") {

+        while ( strcmp( Buffer, "\n" ) != 0 ) {

                 read_4_alignment_lines (Buffer, alignment, fp, get_start_pos);

                 get_start_pos = FALSE; /* read 1rst 4 alignment lines*/

                                         /* already got the starting pos*/

@@ -274,7 +274,7 @@

Index: sift/src/Psiblast.c

===================================================================

--- sift.orig/src/Psiblast.c

+++ sift/src/Psiblast.c

@@ -302,7 +302,7 @@ get_top_seq (char next_seq_to_add[], Has

 	FILE* psiblastfp;

 	char name[KEY_WIDTH];

 	char *strptr;

 	if ((psiblastfp = fopen (psiblastres_file, "r")) == NULL)

--- a/src/clump_output_alignedseq.c

+++ b/src/clump_output_alignedseq.c

@@ -137,7 +137,7 @@

 	char queryfilename[LARGE_BUFF_LENGTH];

 	if (argc < 4) {

-		printf ("clump.c : Clusters sequences into % clus");

+		printf ("clump.c : Clusters sequences into %% clus");

 	}

 	if (argc > 1 ) strcpy (seqfilename, argv[1]);

--- a/src/Matrix_Info.c

+++ b/src/Matrix_Info.c

@@ -467,7 +467,7 @@

 				case 2: /* +- phenotype is - */

 					if ( matrix->weights[aa_atob[c]][l] >= 0) {

 						pos_error_fp++;	error_fp++; 

-		printf ("incorrect less severe %d %d %c\n", l, matrix->weights[aa_atob[c]][l], c);

+		printf ("incorrect less severe %d %g %c\n", l, matrix->weights[aa_atob[c]][l], c);

 						print_type = print_incorrect;

 					} else if (matrix->weights[aa_atob[c]][l] < 0){

 					pos_notobserved_intolerant++;