casa-mp-base

Description: Change class name of _Context_LSS

 New version 1.4 of SeQan uses a different name of the class. 

Forwarded: no

Author: Gert Wollny <gw.fossdev@gmail.com>

Last-Update: 2014-100-06

​

--- diff_sample.h

+++ diff_sample.h

@@ -979,7 +979,7 @@ void DifferenceCoverSample<TStr>::build(

    {

        Timer timer(cout, "  Invoking Larsson-Sadakane on ranks time: ", this->verbose());

        VMSG_NL("  Invoking Larsson-Sadakane on ranks");

-       _Context_LSS<TIndexOff> c;

+       ContextLss_<TIndexOff> c;

        c.suffixsort(

            (TIndexOff*)begin(_isaPrime, Standard()),

            (TIndexOff*)begin(sPrime, Standard()),

Description: Proper type-casting in using seqan::_setBegin().

 Required by newer versions of GCC.

Forwarded: no

Author: Ognyan Kulev <ogi@debian.org>

Last-Update: 2013-04-18

​

--- pat.h

+++ pat.h

@@ -120,13 +120,13 @@

    ~Read() {

        clearAll(); reset();

        // Prevent seqan from trying to free buffers

-       _setBegin(patFw, NULL);

-       _setBegin(patRc, NULL);

-       _setBegin(qual, NULL);

-       _setBegin(patFwRev, NULL);

-       _setBegin(patRcRev, NULL);

-       _setBegin(qualRev, NULL);

-       _setBegin(name, NULL);

+       _setBegin(patFw, (Dna5*)NULL);

+       _setBegin(patRc, (Dna5*)NULL);

+       _setBegin(qual, (char*)NULL);

+       _setBegin(patFwRev, (Dna5*)NULL);

+       _setBegin(patRcRev, (Dna5*)NULL);

+       _setBegin(qualRev, (char*)NULL);

+       _setBegin(name, (char*)NULL);

    }

 #define RESET_BUF(str, buf, typ) _setBegin(str, (typ*)buf); _setLength(str, 0); _setCapacity(str, BUF_SIZE);

Description: Use SeqAn 1.4's seqan::popCount() function instead of own function

Author: Ognyan Kulev <ogi@debian.org>

Last-Update: 2014-03-08

---

This patch header follows DEP-3: http://dep.debian.net/deps/dep3/

--- diff_sample.h

+++ diff_sample.h

@@ -481,6 +481,8 @@ static String<T> getDeltaMap(T v, const

    return amap;

 }

+// Debian: Use seqan::popCount

+#if 0

 /**

  * Return population count (count of all bits set to 1) of i.

  */

@@ -493,6 +495,7 @@ static unsigned int popCount(T i) {