Examples 6 and 9

[domibel]

Please compare bowtie 1.2.1.1 results with the results in the manual:

https://github.com/BenLangmead/bowtie/blob/master/MANUAL

Example 6:
bowtie-1.2.1.1$ ./bowtie -a --best --strata -v 2 --suppress 1,5,6,7 e_coli -c ATGCATCATGCGCCAT
-	gi|110640213|ref|NC_008253.1|	2852852	8:T>A
-	gi|110640213|ref|NC_008253.1|	148810	10:A>G,13:C>G
+	gi|110640213|ref|NC_008253.1|	1093035	2:T>G,15:A>T
-	gi|110640213|ref|NC_008253.1|	905664	6:A>G,7:G>T
-	gi|110640213|ref|NC_008253.1|	4930433	4:G>T,6:C>G
# reads processed: 5
# reads with at least one reported alignment: 5 (100.00%)
# reads that failed to align: 0 (0.00%)
Reported 5 alignments to 1 output stream(s)

Example 9:
bowtie-1.2.1.1$ ./bowtie -a -m 3 --best --strata -v 2 e_coli --suppress 1,5,6,7 -c ATGCATCATGCGCCAT
# reads processed: 1
# reads with at least one reported alignment: 0 (0.00%)
# reads that failed to align: 0 (0.00%)
# reads with alignments suppressed due to -m: 1 (100.00%)
No alignments

[ch4rr0]

Thank you for taking notice of this. We are aware of this issue, and already have fix committed to the bug_fixes branch. The changes will be part of our next release.

[ch4rr0]

This change was included as part of our most recent release.