drop table if exists t1,t2;
create table t1 (
        snp_type varchar (2) not null,
        snp_id int not null,
        chr_cnt int not null,
        contig_cnt int not null,
        loc_cnt int not null,
        weight int not null,
        hap_cnt int not null,
        placed_cnt int not null,
        grouped_cnt int not null,
        unplaced_cnt int not null,
        md5 char (32) null,
        assembly varchar (32) null
) engine = myisam;

create table t2 (
        snp_type varchar (2) not null,
        snp_id int not null,
        chr_cnt int not null,
        contig_cnt int not null,
        loc_cnt int not null,
        weight int not null,
        hap_cnt int not null,
        placed_cnt int not null,
        grouped_cnt int not null,
        unplaced_cnt int not null,
        md5 char (32) null,
        assembly varchar (32) null,
        unique index iuc_rs_weight_assembly using btree (snp_id, assembly),
        index idxsnpid using btree (snp_id, weight),
        index idxmd5 using btree (md5)
) engine = memory;

set @snp_id:=4;
set @assembly:=4;
insert into t1 values ('aa',0,1,1,1,1,1,1,1,1,md5(0),md5(0));
insert into t1 values ('aa',1,1,1,1,1,1,1,1,1,md5(1),md5(1));
insert into t1 values ('aa',2,1,1,1,1,1,1,1,1,md5(2),md5(2));
insert into t1 values ('aa',3,1,1,1,1,1,1,1,1,md5(3),md5(3));
insert into t1 select 'aa',(@snp_id:=@snp_id+1),1,1,1,1,1,1,1,1,md5(@snp_id),md5(@assembly:=@assembly+1)
from t1,t1 a,t1 b,t1 c,t1 d,t1 e,t1 f,t1 g,t1 h,t1 i,t1 j,t1 k,t1 l;




select * from t1 into outfile 't1.txt';
load data infile 't1.txt' into table t2;

results:
--------------

server started like this:
D:\mysql-5.5.29-winx64\bin>mysqld.exe --no-defaults --skip-gr --skip-na --console  --tmp-table-size=20G --max-heap-table-size=20G


mysql> show table status;
+------+--------+---------+------------+----------+----------------+-------------+-----------------+--------------+-----------+----------------+---------------------+---------------------+------------+-------------------+----------+----------------+---------+
| Name | Engine | Version | Row_format | Rows     | Avg_row_length | Data_length | Max_data_length | Index_length | Data_free | Auto_increment | Create_time         | Update_time         | Check_time | Collation         | Checksum | Create_options | Comment |
+------+--------+---------+------------+----------+----------------+-------------+-----------------+--------------+-----------+----------------+---------------------+---------------------+------------+-------------------+----------+----------------+---------+
| t1   | MyISAM |      10 | Dynamic    | 67108868 |            111 |  7516193212 | 281474976710655 |         1024 |         0 |           NULL | 2013-02-03 20:32:57 | 2013-02-03 20:35:47 | NULL       | latin1_swedish_ci |     NULL |                |         |
| t2   | MEMORY |      10 | Fixed      | 67108868 |            105 |  7577280864 |      3534400124 |  11744051900 |         0 |           NULL | 2013-02-03 20:41:32 | NULL                | NULL       | latin1_swedish_ci |     NULL |                |         |
+------+--------+---------+------------+----------+----------------+-------------+-----------------+--------------+-----------+----------------+---------------------+---------------------+------------+-------------------+----------+----------------+---------+
2 rows in set (0.00 sec)