From 6aa99917f8103ef2ce508e00cb1fa6d24d3c667e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Torbj=C3=B8rn=20Rognes?= Date: Wed, 6 Jul 2016 11:34:04 +0200 Subject: [PATCH] Swarm 2.1.9: Fix compilation errors with GCC 6 --- man/swarm.1 | 5 ++++- man/swarm_manual.pdf | Bin 25269 -> 25369 bytes src/search16.cc | 36 ++++++++++++++++++------------------ src/search8.cc | 36 ++++++++++++++++++------------------ src/swarm.h | 2 +- 5 files changed, 41 insertions(+), 38 deletions(-) diff --git a/man/swarm.1 b/man/swarm.1 index b2af08d0..02bbe97f 100644 --- a/man/swarm.1 +++ b/man/swarm.1 @@ -1,5 +1,5 @@ .\" ============================================================================ -.TH swarm 1 "March 11, 2016" "version 2.1.8" "USER COMMANDS" +.TH swarm 1 "July 6, 2016" "version 2.1.9" "USER COMMANDS" .\" ============================================================================ .SH NAME swarm \(em find clusters of nearly-identical nucleotide amplicons @@ -329,6 +329,9 @@ New features and important modifications of \fBswarm\fR (short lived or minor bug releases are not mentioned): .RS .TP +.BR v2.1.9\~ "released July 6, 2016" +Version 2.1.9 fixes errors when compiling with GCC version 6. +.TP .BR v2.1.8\~ "released March 11, 2016" Version 2.1.8 fixes a rare bug triggered when clustering extremely short undereplicated sequences. 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z+|bz49Mk0%Mi>SdT1;k46t1_hM2{Vy36|*20;U5CjMy-=G{7{~(il?==ub4~1B224 zY;QeM7#Uicm||+Sw7?JpracTXLnA|UZv)N43<_YHMOLQ|N?=At2ADBxWPlm7Mn;nz zlY}*mF`a2-VrhitN1#QMYm@Ba+zgFeOby(C3d}7HU5!lL3|-BPEF7K9+>C&3b~CWE hA*dpj%g&CgxFoTtq@pM_jSHAB%}u#fRbBnvxB!RBACv$9 diff --git a/src/search16.cc b/src/search16.cc index 0129a8e3..fffb4116 100644 --- a/src/search16.cc +++ b/src/search16.cc @@ -155,31 +155,31 @@ inline void dprofile_fill16(WORD * dprofile_word, " xorq %%r11, %%r11 \n" #define ONESTEP(H, N, F, V, DIR) \ - " paddusw "V", "H" \n" \ - " movdqa "H", %%xmm13 \n" \ - " pcmpgtw "F", %%xmm13 \n" \ + " paddusw " V ", " H " \n" \ + " movdqa " H ", %%xmm13 \n" \ + " pcmpgtw " F ", %%xmm13 \n" \ " pmovmskb %%xmm13, %%edx \n" \ - " movw %%dx, 0+"DIR" \n" \ - " pminsw "F", "H" \n" \ - " pminsw %%xmm12, "H" \n" \ - " movdqa "H", %%xmm13 \n" \ + " movw %%dx, 0+" DIR " \n" \ + " pminsw " F ", " H " \n" \ + " pminsw %%xmm12, " H " \n" \ + " movdqa " H ", %%xmm13 \n" \ " pcmpeqw %%xmm12, %%xmm13 \n" \ " pmovmskb %%xmm13, %%edx \n" \ - " movw %%dx, 2+"DIR" \n" \ - " movdqa "H", "N" \n" \ - " paddusw %%xmm14, "H" \n" \ - " paddusw %%xmm15, "F" \n" \ + " movw %%dx, 2+" DIR " \n" \ + " movdqa " H ", " N " \n" \ + " paddusw %%xmm14, " H " \n" \ + " paddusw %%xmm15, " F " \n" \ " paddusw %%xmm15, %%xmm12 \n" \ - " movdqa "H", %%xmm13 \n" \ - " pcmpgtw "F", %%xmm13 \n" \ + " movdqa " H ", %%xmm13 \n" \ + " pcmpgtw " F ", %%xmm13 \n" \ " pmovmskb %%xmm13, %%edx \n" \ - " movw %%dx, 4+"DIR" \n" \ - " movdqa "H", %%xmm13 \n" \ + " movw %%dx, 4+" DIR " \n" \ + " movdqa " H ", %%xmm13 \n" \ " pcmpgtw %%xmm12, %%xmm13 \n" \ " pmovmskb %%xmm13, %%edx \n" \ - " movw %%dx, 6+"DIR" \n" \ - " pminsw "H", %%xmm12 \n" \ - " pminsw "H", "F" \n" + " movw %%dx, 6+" DIR " \n" \ + " pminsw " H ", %%xmm12 \n" \ + " pminsw " H ", " F " \n" inline void donormal16(__m128i * Sm, diff --git a/src/search8.cc b/src/search8.cc index e022940c..25a52b5f 100644 --- a/src/search8.cc +++ b/src/search8.cc @@ -443,31 +443,31 @@ inline void dprofile_fill8(BYTE * dprofile, #define ONESTEP(H, N, F, V, DIR) \ - " paddusb "V", "H" \n" \ - " movdqa "H", %%xmm13 \n" \ - " pcmpgtb "F", %%xmm13 \n" \ + " paddusb " V ", " H " \n" \ + " movdqa " H ", %%xmm13 \n" \ + " pcmpgtb " F ", %%xmm13 \n" \ " pmovmskb %%xmm13, %%edx \n" \ - " movw %%dx, 0+"DIR" \n" \ - " pminub "F", "H" \n" \ - " pminub %%xmm12, "H" \n" \ - " movdqa "H", %%xmm13 \n" \ + " movw %%dx, 0+" DIR " \n" \ + " pminub " F ", " H " \n" \ + " pminub %%xmm12, " H " \n" \ + " movdqa " H ", %%xmm13 \n" \ " pcmpeqb %%xmm12, %%xmm13 \n" \ " pmovmskb %%xmm13, %%edx \n" \ - " movw %%dx, 2+"DIR" \n" \ - " movdqa "H", "N" \n" \ - " paddusb %%xmm14, "H" \n" \ - " paddusb %%xmm15, "F" \n" \ + " movw %%dx, 2+" DIR " \n" \ + " movdqa " H ", " N " \n" \ + " paddusb %%xmm14, " H " \n" \ + " paddusb %%xmm15, " F " \n" \ " paddusb %%xmm15, %%xmm12 \n" \ - " movdqa "H", %%xmm13 \n" \ - " pcmpgtb "F", %%xmm13 \n" \ + " movdqa " H ", %%xmm13 \n" \ + " pcmpgtb " F ", %%xmm13 \n" \ " pmovmskb %%xmm13, %%edx \n" \ - " movw %%dx, 4+"DIR" \n" \ - " movdqa "H", %%xmm13 \n" \ + " movw %%dx, 4+" DIR " \n" \ + " movdqa " H ", %%xmm13 \n" \ " pcmpgtb %%xmm12, %%xmm13 \n" \ " pmovmskb %%xmm13, %%edx \n" \ - " movw %%dx, 6+"DIR" \n" \ - " pminub "H", %%xmm12 \n" \ - " pminub "H", "F" \n" + " movw %%dx, 6+" DIR " \n" \ + " pminub " H ", %%xmm12 \n" \ + " pminub " H ", " F " \n" inline void donormal8(__m128i * Sm, __m128i * hep, diff --git a/src/swarm.h b/src/swarm.h index e7eb55f0..2d2dd51f 100644 --- a/src/swarm.h +++ b/src/swarm.h @@ -52,7 +52,7 @@ #define LINE_MAX 2048 #endif -#define SWARM_VERSION "2.1.8" +#define SWARM_VERSION "2.1.9" #define WIDTH 32 #define WIDTH_SHIFT 5 #define BLOCKWIDTH 32