iRODS write problem #168
Description
I've build htslib from develop and also samtools from develop. To get samtools to build once iRODS support was enabled I used:
make HTSDIR=../htslib.git LDFLAGS=-L"$IRODS_HOME/lib/core/obj" LDLIBS="-lRodsAPIs -lgssapi_krb5"
This builds samtools successfully. I can read BAM and CRAM files in iRODS (although not with an index locally or remotely). I can't insert files successfully. A zero length file of the correct name is added to iRODS, but it is marked as being in the resource "demoResc" and consequently non-existent server-side filesystem path.
./samtools view toy.sam -b -o irods:toy.bam
ERROR: readMsgHeader:header read- read 0 bytes, expect 4, status = -4115
ERROR: readAndProcApiReply: readMsgHeader error. status = -4115 status = -4115 SYS_HEADER_READ_LEN_ERR, Operation now in progress
samtools: error closing "irods:toy.bam": -1
ils -L toy.bam
kdj 0 demoResc 0 2015-01-28.13:56 & toy.bam
generic /usr/local/iRODS/Vault/home/kdj/toy.bam