Situation 1) test.same file has the reads in the format they come from Tophat 

1131_1472_555_F5-P2	163	chr1	14409	1	35M	=	14422	0	GCTCAGTTCTTTATTGATTGGTGTGCCGTTTTCTC	ccb`acQOaeb__`[[cca]_\Y`aaRN"!QKGGG	NM:i:0	NH:i:4	CC:Z:chr12	CP:i:91182	XS:A:-
1131_1472_555_F3	83	chr1	14422	1	50M	=	14409	0	TTGATTGGTGTGCCGTTTTCTCTGGAAGCCTCTTAAGAACACAGTGGCGC	VVJFFJ]X=B\TMMHT^S>BYaZX\WZ]VOWb\Q0<b^\\_cb]UZcccc	NM:i:0	NH:i:4	CC:Z:chr12	CP:i:91154	XS:A:-

Situation 2) test.sam, reads in the same order but with no primer extension in the names
1131_1472_555	163	chr1	14409	1	35M	=	14422	0	GCTCAGTTCTTTATTGATTGGTGTGCCGTTTTCTC	ccb`acQOaeb__`[[cca]_\Y`aaRN"!QKGGG	NM:i:0	NH:i:4	CC:Z:chr12	CP:i:91182	XS:A:-
1131_1472_555	83	chr1	14422	1	50M	=	14409	0	TTGATTGGTGTGCCGTTTTCTCTGGAAGCCTCTTAAGAACACAGTGGCGC	VVJFFJ]X=B\TMMHT^S>BYaZX\WZ]VOWb\Q0<b^\\_cb]UZcccc	NM:i:0	NH:i:4	CC:Z:chr12	CP:i:91154	XS:A:-

Situation 3) test.sam, change mates around, so "forward" comes first
1131_1472_555	83	chr1	14422	1	50M	=	14409	0	TTGATTGGTGTGCCGTTTTCTCTGGAAGCCTCTTAAGAACACAGTGGCGC	VVJFFJ]X=B\TMMHT^S>BYaZX\WZ]VOWb\Q0<b^\\_cb]UZcccc	NM:i:0	NH:i:4	CC:Z:chr12	CP:i:91154	XS:A:-
1131_1472_555	163	chr1	14409	1	35M	=	14422	0	GCTCAGTTCTTTATTGATTGGTGTGCCGTTTTCTC	ccb`acQOaeb__`[[cca]_\Y`aaRN"!QKGGG	NM:i:0	NH:i:4	CC:Z:chr12	CP:i:91182	XS:A:-