Problems with samtools-0.19.0 (MingW)

[Seqwince]

I got the program to compile without error in MingW, simply by adding a few words to the Makefile and hitting Make:

• Iwin32 to INCLUDES
• -Lwin32 -L. -lbam -lm -lz -lpthread -lws2_32 to samtools:lib-recur cmd

Samtools 0.18.0 compiles perfectly like this (although on some systems you have to substitute "lpdcurses" with "lcurses")

However, although samtools 0.19.0 works fine in some limited capacity, it has some problems. For instance, on the example:
samtools faidx examples/ex1.fa
samtools import examples/ex1.fa.fai examples/ex1.sam.gz ex1.bam
samtools index ex1.bam

It fails on this last line with
"[bam_index_core] truncated file? Continue anyway. (-2)"
Is this a problem with the indexer (i.e. the third command), or a problem with the index itself (i.e. the "import" command)?

[edit]
Solved. That was dumb of me. Just start with a clean MinGW instead of using someone else's.

[dpryan]

FYI, "samtools import" has been deprecated for a while. Use "samtools view -Sbo ex1.bam examples/ex1.sam" (unless you actually do need to reheader the BAM file, in which case there's the -t option). At the moment, the "import" command just runs "view", but I wouldn't be surprised if that gets dropped eventually (not to mention that "view" is more flexible).