Commit 6dff5191 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 0.0+git20200121.ba14f430+dfsg

parent c5fea178

src/blat/version.doc

+2 −0
Original line number Diff line number Diff line
@@ -2,6 +2,8 @@ 
     o (in 36x1) Fixed problem with -fastMap option that made it put in gaps in the

       allignment sometimes when a short mismatch would be a better choice.

     o (in 36x2) Fixed problem with -maxIntron set to non-default value on protein query.

     o (in 36x3) Added ipv6 support.

     o (in 36x4) Added _alt support.



36:

     o (in 35x1) added repMatch default values for tileSizes 16 to 18 in genoFind.c

src/blatz/server.c

+5 −3
Original line number Diff line number Diff line
@@ -20,7 +20,8 @@ 
int port = bzpDefaultPort;

int cpuCount = 2;

char *host = "localhost";

unsigned char subnet[4] = {255,255,255,255};



struct cidr *subnet = NULL;



void usage()

/* Explain usage and exit. */
@@ -38,7 +39,8 @@ printf("Options: (defaults are shown for numerical parameters)\n"); 
bzpServerOptionsHelp(bzp);

bzpClientOptionsHelp(bzp);

printf("  -debug Writes diagnostic output to console and no daemon fork\n");

printf("  -subnet=255.255.255.255 Restrict access to subnet\n");

printf("  -subnet=255.255.255.255 Restrict access to subnet. \n");

printf("    Supports comma-separated list of IPv4 or IPv6 subnets in CIDR notation, e.g. 255.255.255.255/24\n");

printf("  -port=%d Use specified TCP/IP port\n", bzpDefaultPort);

printf("  -host=%s Query specified host\n", host);

printf("  -cpu=%d Use specified number of CPUs (processes)\n", cpuCount);
@@ -314,7 +316,7 @@ setMaxAlloc(2LL*1024LL*1024LL*1024LL); 
optionInit(&argc, argv, options);

port = optionInt("port", port);

host = optionVal("host", host);

netParseSubnet(optionVal("subnet", NULL), subnet);

subnet = internetParseSubnetCidr(optionVal("subnet", NULL));

cpuCount = optionInt("cpu", cpuCount);

if (argc < 2)

    usage();

src/htslib/knetfile.c

+5 −0
Original line number Diff line number Diff line
@@ -198,6 +198,11 @@ static SOCKET socket_connect(const char *host, const char *port) 
	server.sin_port = htons(atoi(port));

	if (connect(fd, (struct sockaddr*)&server, sizeof(server)) != 0) __err_connect("connect");

	// freehostent(hp); // strangely in MSDN, hp is NOT freed (memory leak?!)



	/* FOR CODE TO CONNECT SUPPORTING IPV6 and IPV4 using our net.c:

	fd = netConnect(host, port);

	*/



	return fd;

}

#endif

src/htslib/vcf.c

+6 −2
Original line number Diff line number Diff line
@@ -2099,7 +2099,9 @@ int vcf_format(const bcf_hdr_t *h, const bcf1_t *v, kstring_t *s) 
        for (i = 0; i < v->n_info; ++i) {

            bcf_info_t *z = &v->d.info[i];

            if ( !z->vptr ) continue;

            if ( !first ) kputc(';', s); first = 0;

            if ( !first )  

                kputc(';', s); 

            first = 0; 

            kputs(h->id[BCF_DT_ID][z->key].key, s);

            if (z->len <= 0) continue;

            kputc('=', s);
@@ -2146,7 +2148,9 @@ int vcf_format(const bcf_hdr_t *h, const bcf1_t *v, kstring_t *s) 
                for (i = 0; i < (int)v->n_fmt; ++i) {

                    bcf_fmt_t *f = &fmt[i];

                    if ( !f->p ) continue;

                    if (!first) kputc(':', s); first = 0;

                    if (!first) 

                        kputc(':', s); 

                    first = 0;

                    if (gt_i == i)

                        bcf_format_gt(f,j,s);

                    else

src/inc/bamFile.h

+7 −0
Original line number Diff line number Diff line
@@ -50,6 +50,13 @@ samfile_t *bamMustOpenLocal(char *fileName, char *mode, void *extraHeader); 
 * The implementation is just a wrapper around samopen from the samtools library

 * that aborts with error message if there's a problem with the open. */



long long bamFileItemCount(char *fileOrUrl, char *baiFileOrUrl);

/* Return the total number of mapped items across all sequences in fileOrUrl, using index file.

 * If baiFileOrUrl is NULL, the index file is assumed to be fileOrUrl.bai.

 * NOTE: not all bam index files include mapped item counts, so this may return 0 even for large

 * bam.  As of May 2019, our copy of hts_idx_get_stat does not support cram indexes

 * (perhaps they never include counts?), so this always returns 0 for cram. */



void bamFetchAlreadyOpen(samfile_t *samfile, bam_hdr_t *header,  bam_index_t *idx, char *bamFileName, 

			 char *position, bam_fetch_f callbackFunc, void *callbackData);

/* With the open bam file, return items the same way with the callbacks as with bamFetch() */